The story begins with pure white. Suddenly, a hole with stars and planets expands in white, blank "room", and expanding faster and faster until the screen is filled with space.
We cut to a flash back of the original Space Crisis, back when the Primids were attacking. A Imperium fleet is heading towards Earth but is suddenly attacked by a mysterious monster that spits out blue flames.
The Imperium are destroyed by the monster, explaining their absence for the rest of the Space Crisis.
We then flash back to a lightning storm in space, where the USS Kelvin is investigating. The Narada, a Romulan ship attacks the USS Kelvin. Narada's first officer, Ayel, demands that the Kelvin's Captain Robau come aboard to negotiate a truce. Once aboard, Robau is questioned about an "Ambassador Spock", whom he professes not to know, and the current stardate. Narada's commander, Nero, kills him, and continues his attack on the Kelvin. George Kirk, the Kelvin's first officer, orders the ship's personnel, including his pregnant wife Winona, to evacuate the ship while he pilots the Kelvin on a collision course with the Narada. At the cost of his life, Kirk ensures Winona's survival, and she gives birth to their son, James T. Kirk.
In 2250, on the planet Vulcan, a young Spock is accepted to join the Vulcan Science Academy. Realizing that the Academy views his human mother Amanda Grayson as a "disadvantage", he decides to join Starfleet instead. On Earth, Kirk becomes a reckless but intelligent young adult. In 2255, after a bar fight with Starfleet cadets accompanying Nyota Uhura, Kirk meets Captain Christopher Pike who encourages him to enlist in Starfleet Academy where Kirk meets and befriends the cynical doctor Leonard McCoy.
Three years later, Commander Spock accuses Kirk of cheating during his Kobayashi Maru simulation. Kirk argues that cheating was acceptable in this context because the simulation had been designed to be unbeatable. The disciplinary hearing is interrupted by a distress signal from Vulcan. With the primary fleet out of range, the cadets are mobilized. McCoy and Kirk board Pike's ship, the Enterprise.
CHAPTER ONE: THE FUSING
It cuts forward to the present time, in the Mushroom Kingdom where Mario and Luigi find themselves alive again. They find that not only is their universe whole again but that most of the Mushroom Kingdom enemies have fused with each other.
Mario and Luigi meet up with Sonic and Tails, who tell them the fused creatures are in their location as well. They then meet Ganondorf, who tells them that he is working with the Fusionist, who not only fused their dimensions together again but is planning to take over it as a cohesive whole and that he has asked Ganondorf to take out some of the heroes to fuse together as one of his minions. Mario and the other fight Ganondorf and he soon disappears into the shadow.
R.O.B discovers that the floating island where his people lived is some how back, and he decides to lead his people again.
Touko finds the labatory and goes up against Scientist Nathan. Once he looses, he releases Genesect, who proceeds to attack Nathan and then attack Touko.
After defeating Genesect and turning it into a trophy, Touko attempts to capture it but the trophy is taken by Yzma and Kronk. Touko sends out her Pokemon to chase them down.
A strange ship proceeds to let Yzma and Kronk inside, and Touko's pokemon are locked out and can only watch as the strange ship flies away.
Ness hears a loud sound come from outside. After going to crash site on top of the hill, it turns out to be Zim's ship. Ness proceeds to fight Zim.
Zim is defeated and turned into a trophy, but not before Dib takes it for himself. Dib jumps down the hill and Ness proceeds to walk home.
Mario, Luigi, Sonic, and Tails head to Peach's castle to tell her about the fused creatures, but they discover that Bowser (using a cat suit) has captured her. They must defeat him and save Peach.
After defeating Meowser, they tell Peach about the fused creatures. Peach tells them that they must all go to Palutena to see if she can get a read of there they're coming from. They get into karts and head off.
Zelda and Link come across the fused creatures popping up around Hyrule. Ganondorf comes down and fights Link and Zelda, but they defeat him pretty easily. He once again disappears after being beat a second time.
In the distance, a strange machine rises.
Mario, Sonic, Luigi, Tails, and Peach all arrive at Skyworld. Meeting up with Pit and Palutena, they tell them the situation unfolding. Palutena is able to locate that the fused creatures are coming from the Labyrinth of Deceit. However, she is unable to fully track it’s location, as it has made the appearance of being everywhere at once.
Fused creatures begin attacking Skyworld, so the Fighters of Lapis head off to beat them.
Dipper and Mabel are watching TV when they hear someone breaking in. Grunkle Stan comes in to find Lil’ Gideon trying to steal the deed for the shack. After kicking him out, he decides to summon Bill Cipher. Bill Cipher signs a deal with Gideon. Bill agrees to invade Stan's mindscape for Gideon, after making sure that he also will help him on another unspecified project of his own. However, their plans are overheard by Mabel and Soos and they report the situation to Dipper.
Bill Cipher invades Grunkle Stan’s mind and they must go inside. Inside they find the war from Fighters of Lapis 3, with everything frozen in time as Tabuu prepares to unleash a black hole. Bill Cipher appears and the twins fight Bill Cipher but loose as Bill teleports away.
Sora and Riku see a "dark tear" being opened up by some kind of machine. Riku and Sora scale the gigantic machine crawling with Heartless.
As they approach the top, heartless pour out from the dark tear and Sora and Riku must fight them off. Axel appears as the Heartless are defeated and challenge them both. Sora and Riku defeat him and watch him die.
More giant machines crawling with Heartless begin to rise from the ground. As we focus on Springfield, Homer Simpson is relaxing on his lawn about to eat a doughnut as one of the machine rises from the ground, it's antennae grabbing the doughnut. As Homer stands back as it rises, he runs towards it and begins to scale it.
As he approaches the top he is challenged by Kool Aid Man, who attacks by charging and running through the structure. As Homer grabs his doughnut, Kool-Aid man chases him down as he climbs down from the tower, causing the structure to be slowly destroyed.
The Fighters of Lapis fight off the fused creatures but see a dark tear form. They enter inside and are pushed out into another tear inside the dark dimension and land on LEGO Planet, landing on a Dark Tower. They destroy the dimension ripper and head down the Dark Tower to meet Lego Han Solo who is fighting off the Heartless. Palutena suddenly gets a reading of where the Labyrinth is, but the Fighters of Lapis are grabbed by two Klingons and are knocked out by gas. They are put inside the Solar Sailor and it goes off somewhere… far away…
Mordecai and Rigby are up on the roof when they see a Dark Tower rise in the distance and begins ripping open a dimension. Mordecai and Rigby head towards the Dark Tower and begin to climb it to see if they can touch the Dark Tear.
As they reach the top, they come face to face with Robirdo. As they defeat the robotic Birdo, Rigby goes to touch the Dark Tear and gets pulled in by the Heartless. Mordecai follows him and they are knocked out and put into the Solar Sailor.
Homer is knocked out along with Sora and Riku in their respective places. They are pulled into the Solar Salior as it speeds off into space and into a gigantic, planetsized coliseum.
Mario, Luigi, Sonic, Tails, Peach, Palutena, Pit, Lego Han Solo, Sora, Riku, Homer Simpson, Mordecai and Rigby wake up in a cell. There, Ganondorf tells them they are trapped in a fighting tournament and that they will have to fight for their surivial. When asked what any of this had to with the Dark Towers, Ganondorf tells them that he was using the Dark Towers to gather the Fighters so he could determine the best Fighters and fuse them together.
However there is no time to protest. Mario and Sonic go up against Link and Zelda. After turning them into trophies, they move onto the AVGN and the Nostalgia Critic.
As the fight continues, the strange ship hosting Yzma and Kronk lands. As they exit, they meet Samus. Kronk fights Samus and is turned into a trophy. Yzma runs to tell her superiors as Samus frees the Kronk trophy.
The Tournament II
Pit and Palutena face off Finn and Jake and Quote and Curly, turning them into trophies. As the Tournament continues, it comes down to just two teams: Sonic & Mario and Pit and Palutena. Samus and Kronk suddenly come down into the match and the four stop fighting. Ganondorf comes out into the tournament and attempts to fight Samus but Kronk takes him out in a hit, turning him into a trophy.
Samus then takes out Mario, Sonic, Pit, and Palutena and turns them into trophies. She takes all the trophies and places them in her ship. She has a destination she needs to go to. And she needs all the people she can get.
As Samus' ship travels through space, she comes across a hostile ship. Opening up communications she discovers it is Zim's spaceship, but Dib is speaking. Samus stops her ship and jumps through space and breaks and enters into the ship to fight Dib. She takes out Dib and grabs the Zim and Dib trophies and straps Zim's ship to her own.
Grunkle Stan's Mind
As Dipper and Mabel continue going through the frozen battlefield they discover a door of memories of Dipper as they continue searching for the memory of the vault. Dipper slips into the door and discovers the reason why Grunkle Stan doesn't like him.
As Mabel and Soos keep searching, they come across the vault memory. Suddenly the real Soos shows up and the Soos that was with Mabel turns into Bill. Soos and Mabel fight off Bill Cipher again, but fail as he zooms away. Just then Mabel shoots the door into Tabuu's hands which are forming a black hole, and the door disappears forever.
Bill gets mad and sends them into his own little fighting area.
Samus' ship approaches the Narada that is flying near Vulcan. She notes the Enterprise and frees the crew as they note the drill that is opening up to the core.
Samus and the others land on the drill where Kirk and Sulu are, helping them out with the fight. They shut down the drill but it is too late as red matter is launched into the core anyway. Suddenly Samus' ship is shot down by Yzma;s ship and she and the other fighters must go onto the Enterprise with Kirk and Spock.
Palutena tells the Enterprise to travel to the Labyrinth of Deceit, telling them that they need to take down the Narada later.
Labyrinth of Deceit
Mario, Pit, Palutena, Samus, Patrica Wagon, and Peach all head inside the Labyrinth of Deciet. They fight their way through Underworld and Heartless forces. At the end they encounter Pandora. She tells them about the mirrors of truth and how they work. She notes she has six as opposed to one, although refuses to tell why.
During the fight they defeat Pandora and destroy the mirrors but don't realize they have let out their dark sides. The dark versions of the characters finish off Pandora and Dark Pit steals her powers and flies off with the rest of the dark duplicates.
CHAPTER 2: MIRROR MATCH
The Dark World
As they exit the Labyrinth of Deceit and come back to the Enterprise, Palutena tracks the location of the Dark Duplicates. Believing they need to be stopped, Palutena tracks their location to a nightmarish dimension called the Dark World.
In the Dark World, they meet Mike Dawson in a cell. They free him and they find the Dark Duplicates hanging out. Palutena attacks Dark Palutena and wins the fight, but the other Dark Duplicates grab Dark Palutena’s trophy and revive her; escaping the nightmarish dimension. Palutena exits and will worry about them later.
Steve, who awakes with a case of amnesia in a strange town in 1953 called Harvest. He can't remember anything from his past and when he tells the people that claim to be his family, as well as townsfolk, they all tell him what a kidder he is. All of the town inhabitants are extremely eccentric and many appear to be more a satire or stereotype than real people. They all continuously stress to Steve that he should join the Lodge, which is a large building located at the center of town that serves as the headquarters of the Order of the Harvest Moon. Steve visits the Sergeant at Arms at the Lodge, who tells him that all of his questions will be answered inside the building. To enter, he must first join the Order of the Harvest Moon. But in order to join, he must perform a series of tasks that range from simple vandalism to arson for his initiation.
After doing these tasks he enters the Lodge. There he finds Roxas who was also put into the same task as well. He explains that he has amnesia as well, and, like Steve, notices that something doesn't seem right about the town.
The two meet the head of the Harvest Order, the Grand Muckity Muck, shares a few short words with Steve, and then attacks him. Steve successfully defeats the Grand Muckity Muck and meets the Sergeant at Arms one last time.
He explains to Steve that everything in Harvest is created by a virtual reality simulator, which he and Roxas are hooked up to. The Sergeant at Arms explains that this simulation was created in hopes of successfully turning Steve into a serial killer in real life. Steve and Roxas notice a computer in the room and destroy it, ending the stimulation, however they are stuck in a strange room with a doctor named Valentine.
The Ruins of Another World
Meanwhile, the Dark Towers rise in Unova too, opening up Dark Tears for Heartless to pop out of. Touko is trying to fight off the Heartless but most of her Pokemon have fainted, leaving her with just Snivy. As the Heartless close in on Touko, a Pokeball zips through the air with Meowstic coming out to battle. Serena helps fight off the Heartless with Touko.
Serena and Touko scale a dark tower and head into the Dark Tear where they land in a desert somewhere...
Grunkle Stan's Mind II
Meanwhile, as Dipper searches for an exit, he comes across the memory of Stan expressing his actual feelings toward Dipper, and after watching the rest of the memory, learns that Stan is only hard on him to prepare him to face the world. However, he is sucked into the memory, and the Stan within the recollection informs Dipper of the ability to do whatever he wants within the mind.
Dipper then realizes that he must stop Bill and rushes off. As the demon is torturing Mabel and Soos with their nightmares (a British dog man for Soos, and making Mabel ugly) and prepares to finish them off once and for all, Dipper arrives with the news of being able to make dreams reality and demonstrates the ability to his comrades via laser vision. Mabel decides to give herself the ability to shoot kitten heads from her arms, Soos utilizes a question mark beam from his stomach, and so forth. Just as Soos, the twins, and Mabel's dream boys are about to send Bill out of Stan's head, he stops them, warns them of an approaching evil, and leaves. Stan wakes up and thereby forces Soos and the twins out of his head. They are relieved to have been rid of Bill, but their relief is cut short as Gideon reveals that he used dynamite to obtain the deed to the Shack, which gives him ownership according to Gravity Falls' odd laws, and forces the "trespassers" out as he has Bud destroy the building.
Meanwhile, Shantae is shopping when she meets street rat Aladdin and his monkey, Abu, and the two begin to form a friendship. After Aladdin is arrested for thievery, he meets a elderly man who tells him to go into the Cave of Wonders, promising a reward in return for retrieving the lamp.
The tiger-shaped head of the cave allows them to enter but warns them to touch nothing but the lamp. Aladdin and Abu find a magic carpet. Aladdin obtains the lamp but Abu's attempt to steal a gem backfires and causes the cave to collapse. The carpet flies them back to the entrance and Aladdin delivers the lamp to Jafar, who then tries to kill him. Abu then thwarts Jafar and steals back the lamp as he, the carpet, and Aladdin fall back into the cave just as it closes.
In the collapsed cave, Aladdin rubs the lamp, unexpectedly unleashing Genie, who reveals he will grant Aladdin three wishes—with the exception of murder, romance, revival of the dead, or additional wishes. Aladdin tricks the genie into magically freeing himself, Abu, and the Carpet from the cave without actually using a wish; thereafter, Genie states that Aladdin will not receive anymore magic help unless he explicitly states "I wish". While contemplating his wishes, Genie admits he would wish for freedom, since he is a prisoner to his lamp. Aladdin promises to free Genie as his last wish.
Lawyer John Reid is returning home via the uncompleted Transcontinental Railroad, managed by railroad tycoon Latham Cole. Unknown to Reid, the train is also carrying Tonto and outlaw Butch Cavendish, who is being transported for his hanging after being captured by Dan Reid, John's Texas Ranger brother. Cavendish's gang rescues Butch and derails the train. Tonto is subsequently jailed. Dan deputizes John as a Texas Ranger, and with six others they go after the Cavendish gang.
Cavendish's men ambush and kill their pursuers in a canyon and Cavendish cuts out and eats Dan's heart. Tonto, who has escaped from jail, comes across the dead men and buries them. However, a white spirit horse awakens John as a "spirit walker," and Tonto explains John cannot be killed in battle. Tonto also tells him Collins, one of the Rangers, betrayed Dan and is working with Cavendish, whom Tonto believes is a "wendigo." As John is thought to be dead, he wears a mask to protect his identity from enemies. Tonto gives John a silver bullet made from the fallen Rangers' badges and tells him to use it on Cavendish.
As the Narada heads toward Earth, Nero tortures Pike to gain access to Earth's defenses, and Kirk is stranded on Delta Vega after attempting mutiny. Kirk encounters an older Spock, who explains that he and Nero are from 129 years into the future when Romulus was threatened by a supernova. Spock's attempt to use "red matter" to create an artificial black hole and consume the supernova was too late, and Nero's family perished along with Romulus. Narada and Spock's vessel were caught in the black hole, sending them back in time. Nero stranded Spock on Delta Vega to watch Vulcan's destruction as revenge for failing to save Romulus.
Spock then realizes that Mario was talking about something similar with black holes. Could black holes send things back in time?
Reaching a Starfleet outpost, Kirk and Spock Prime meet Montgomery Scott. With the elder Spock's help, Kirk and Scott beam onto the Enterprise. Following the elder Spock's advice, Kirk provokes Spock into attacking him, leading Spock to relinquish command due to being emotionally compromised. After talking with Sarek, Spock decides to help Kirk.
Shantae meets up with Aladdin again. Apparently Risky plans to attack Agrabah and Sequin Town, so they must stop her by going to sea.
After getting a boat and a crew they head out to sea. During a storm, Will Smith Fish comes on board and attacks. After his defeat, Octomug attacks the ship, giving Toon Sonya and Korra the ability to showcase their skills. Will Smith Fish delivers the final blow, being freed from trophy form.
They arrive on Risky's ship, where Toon Subzero attacks. After defeating him, Risky proceeds to give up but grabs Aladdin and drowns him.
Aladdin uses his second wish to get out.
The Narada approaches Earth. While Enterprise hides itself under the gas clouds of Titan, Kirk, Spock, Mario, Palutena, Pit, Patrica Wagon, Peach, Samus, and Sonic all beam aboard the Narada.
The Romulan ship arrives at Earth and deploys its drilling rig directly over San Francisco. Scotty thought he would be beaming The Fighters of Lapis to the Narada's cargo bay, but it turns out to be a heavily occupied portion of the ship. After a brief firefight, Spock uncovers the location of the black hole device and Captain Pike by melding with an unconscious Romulan. When they board the Jellyfish, it recognizes Spock as its captain (at which Kirk sarcastically expresses surprise), and the Vulcan finally figures out what is going on, as the ship's computer confirms its origin stardate as 2387, constructed by the Vulcan Science Academy. Spock confronts Kirk about withholding information from him, but Kirk dodges the question by asking Spock if he can fly the spacecraft, a question he is fairly confident Kirk already knows the answer to.
The Dark Duplicates show up and attack their doubles, leaving Spock, Kirk and Sonic the only members of the team that can pull the plan off.
As Spock commandeers the Jellyfish and blasts out of the Narada, Kirk runs into more trouble as he finds the Romulans' "bridge", where Nero and Ayel are waiting. Kirk is confronted by Nero, who has recognized him from Earth's history, and after a brief scuffle, Nero pins Kirk and tells him that, while he was a decorated officer and went on to captain the starship Enterprise, that was another life, and that he plans to deprive him of the same life his father once had. Before he can finish Kirk off, however, Nero is informed that the Jellyfish has been stolen and the drill has been destroyed. Furious above all else, Nero storms off, leaving Kirk to Ayel while he plans to kill Spock. Ayel promptly grabs Kirk by the throat and lifts him in the air, surprised at how "weak" Humans appear to be. Seeing his prey attempting to talk, Ayel offers Kirk the chance to say something – and the Human replies that he is in possession of the Romulan's disruptor pistol. Kirk fires and kills Ayel as he plunges into the depths of the Romulan vessel. He then heads off to rescue Pike.
On the bridge, Nero hails Spock, declaring that he should have killed him when he had the chance. In reply, Spock taunts Nero by "ordering" him to surrender. Nero orders the Jellyfish destroyed, even though the ship still has "red matter" on it; with his plan for revenge ruined, now he only wants to kill Spock. The Jellyfish evades the missiles, then goes into warp, with Nero and the Narada in hot pursuit, leaving Earth behind.
When the ships drop out of warp, the Jellyfish turns to intercept and collide with the Narada, seeking to ignite the red matter and create a hole that will envelop both ships. Nero panics and orders all weapons fired, but the Enterprise arrives on the scene and destroys the missiles with a fierce volley of its phasers, allowing Spock to carry through with his plan to ram the Narada.
Inside the Narada, Kirk finds Pike, alive but injured due to his earlier torture. Pike is quite surprised, but Kirk reminds him of his previous order to "come and get me", and when two Romulan soldiers walk in and find Kirk, effectively defenseless while freeing Pike from the chamber, the captain returns the favor, grabbing the gun on Kirk's belt and killing the intruders before his rescuer even realizes what happened. Scotty successfully beams back Kirk, Pike, Mario, Palutena, Pit, Patrica Wagon, Peach, Samus, Sonic and Spock, right before the Jellyfish collides with the Narada.
The explosion of the Jellyfish ignites the entire stockpile of "red matter" on board, creating a black hole, which begins to swallow up the Narada. To Spock's surprise, Kirk offers to rescue the surviving crew, arguing that this might improve long-term relations between the Romulans and the Federation, and is thus only "logical." Spock, mindful that Nero is the man who destroyed his planet and murdered his mother, coolly suggests that they dispense with logic in this case. Their debate is ended when Nero, belligerent to the last, says he prefers to die in agony than accept help from them. Kirk obliges and orders Sulu to fire all weapons, blowing the ship apart with phasers and photon torpedoes. The Narada is finally destroyed, but the gravitational pull of the black hole begins tugging on the Enterprise, keeping it from escaping, even with its engines running at warp speed. The pressure is heavily damaging the ship as Kirk orders Scott to get them out of there at all cost.
CHAPTER 3: BATTLE AGAINST THE FUSIONIST
The World That Never Was
Just as the Enterprise exits the scene it is plunged into a dark tear. The Enterprise crashes into a city swarming with Heartlesses and Nobodies. And there... Dark Samus awaits.
Samus takes on her dark side and seemingly destroys Dark Samus for good. Blue phazon leaks out of the wreckage, and Zero Suit Dark Samus attacks. Samus defeats this form too, tossing the trophy into a chasm.
There they meet Axel again, under the name of Lea. His heart had returned to his real body and he agrees to help the Fighters of Lapis take down the Fusionist and his forces. They enter the Castle that Never Was.
Aladdin has second thoughts about freeing Genie, believing that without him he is "just Aladdin". Iago steals the lamp and brings it to Jafar. Jafar becomes Genie's new master, using his first two wishes to usurp the Sultan's throne and become the most powerful sorcerer in the world. Using his new powers, Jafar enslaves Jasmine and the Sultan, exposes Aladdin as a street rat, then exiles him and Abu to a frozen wasteland.
Aladdin and Abu use the magic carpet to return to the palace, where Aladdin sneaks in to try and recapture the lamp. Jafar proposes using his third wish to make Jasmine his queen. Genie protests that he cannot grant that wish, but Jasmine decided to feign interest in Jafar, allowing Aladdin to try to grab the lamp. Aladdin gets caught and battles Jafar, who transforms himself into an enormous cobra and traps Aladdin.
Just then, Shantae, Toon Sonya, Will Smith Fish, and Korra come in and free Aladdin. They fight Jafar's giant cobra form. After defeating it, the Irate Gamer shows up and complains that it wasn't climatic enough, wishing it was harder. The Genie over-hears this and revives Jafar and makes him into a giant scorpion.
After defeating Jafar once again, the world returns to normal.
The Tournament III
Meanwhile on the Tournament Planet, Valentine releases Steve and Roxas to do one last battle in the tournament, with the intention of fusing the winner with McDonald Miku. Yzma and Valentine watch as Steve and Roxas fight, but then Steve throws a hatchet at the eletrical power supply, turning down all the power on the Tournament Planet.
McDonald Miku chases them in the dark however, intending to fuse them both with herself. After fighting McDonald Miku they steal Yzma's ship, however Valentine begs them to take her off the planet before the fused abominations get her. They comply and leave the planet, heading to the Fusionist's Lair using Valentine's instructions.
At a brothel Collins recently visited, Red Harrington informs them about Dan and Collins' fight over a cursed silver rock. Meanwhile, Cavendish's men, disguised as Comanches, raid frontier settlements. John and Tonto arrive after raiders abduct Dan's widow and son, Rebecca and Danny. Regretting his earlier actions, Collins attempts to help Rebecca and Danny escape but is shot dead by Cole, who rescues them. Claiming the raiders are hostile Comanches, Cole announces the continued construction of the railroad and dispatches United States Cavalry Captain Jay Fuller to exterminate the Native Americans.
A Comanche tribe captures John and Tonto soon after the pair finds railroad tracks in Indian territory. The tribe leader tells John of Tonto's past: As a boy, Tonto had rescued Cavendish and another man from near-death and showed them the location of a silver mine, in exchange for a pocket watch. The men murdered the tribe to keep the mine a secret, leaving Tonto with great guilt.
Tonto and John escape as the cavalry attack the Comanche. At the silver mine, they capture Cavendish. Tonto demands that John use the silver bullet to kill Cavendish, but John refuses. Tonto attempts to kill Cavendish, but John knocks him unconscious and brings in Cavendish alive. Upon returning Cavendish to Cole and Fuller's custody, Cole is revealed to be Cavendish's partner. Fearing that if his actions are publicly revealed he'll be charged as a war criminal, Fuller sides with Cole. Rebecca is held hostage, and John is taken back to the silver mine to be executed. However, Tonto rescues him and the two flee as the Comanche attack and are massacred by the cavalry. Realizing that Cole is too powerful to be taken down lawfully, John dons the mask again.
At the site of the union of the Transcontinental Railroad, Cole reveals his true plan: to take complete control of the railroad company and use the mined silver to gain more power. John and Tonto steal nitroglycerin and use it to destroy a railroad bridge. With Red's help, Tonto steals the train with the silver, and Cole, Cavendish and Fuller pursue him in a second train on which Rebecca and Dan Jr. are being held captive. Riding Silver, John pursues both trains. After a furious chase and fights on both trains, both Cavendish and Fuller are killed, Rebecca and Dan Jr. are rescued and Cole dies buried beneath the silver ore after the train plunges off the severed bridge and into the river below.
Agent Coulson appears on the scene where the Lone Ranger and Tonto are and tell them they are needed to stop a even bigger threat. The Lone Ranger and Tonto ride on Silver as Agent Coulson opens up a portal to the Castle That Never Was.
The Castle That Never Was
The fighters arrive in the Castle That Never Was fighting off nobodies and heartless. They are greeted by Zerina who attacks them. After defeating Zerina, they meet the Shadow Queen who blocks them from going further. After defeating her and chucking her trophy into the chasm, they keep going in until they enter the Fusionist's Lair.
The Fusionist's Lair
They meet the guardian of the Fusionist's lair: Robosaur. They easily defeat Robosaur and head in further where they meet Dark Patrica Wagon, Dark Pit, and Dark Palutena who join their forces to stop the Fusionist. They show Sora and Riku that Kairi was locked up here and free her.
They find a heavily locked door and bust it down, expecting to find the Fusionist. Instead they find a girl named Namine.
All the residents of Gravity Falls are waiting outside of the Mystery Shack, excited for what Gideon has in store for them and the shack. In the background, the camera zooms in on Mabel, Dipper, Soos and Grunkle Stan in disguise, thinking of a way to get the deed back.
Gideon comes out of the shack, greeting the huge crowd in front of him. After a short speech, he reveals his plans to build a brand new Gideon-themed amusement park, dubbed "Gideonland." The Pines family and Soos gasp upon hearing the announcement. Gideon then shows Waddles dressed up as Gideon, making Waddles a new attraction and "Gideonland's" mascot. Mabel then screams and calls Gideon a monster.
The group then charges onto the stage, trying to convince everyone that Gideon is a fraud and that he stole the deed to the shack and should be arrested. Gideon walks up to them, and tells everyone that he has proof that Stan gave him the deed, and pulls it out of his suit. Sheriff Blubs believes Gideon.
Dipper, Mabel, and Stan are kicked off the stage and the property of the shack by two guards, much to Gideon's delight.
After getting kicked out, Soos and the Pines Family are stranded outside of the fence, glumly watching as Gideon speaks more about his plot for "Gideonland".
Back at Soos' house, Mabel is worried on where they would stay, with Soos reminding her that Stan always has something figured out. Stan calls Dipper and Mabel's parents, saying where there are, lying by saying that they are in a "Four star hotel," despite the ruined state the house is in.
Meanwhile at the Mystery Shack, Gideon is seen looking through the contents of Journal 2. Waddles tries to escape through the window, but cowers in a corner due to Gideon's pig whistle and looks on, trembling in fear. Gideon's father arrives and tells him that he should be celebrating Gideonland instead on looking at the book. Gideon tells his father the true nature of this book, saying it was written many years ago by a brilliant unknown author who learned secrets too powerful for one man, and hid the journals where no one could find them, because he knew that when the journals are brought together, it would lead to a gateway of "unimaginable power". Gideon says that codes and maps from the journal have led him to believe that the other book is hidden somewhere on the Shack's property and is determined to find it.
While Dipper, Mabel, and Soos are playing with toy cars, Stan arrives and tells the kids that he can't take care of them anymore and that they'll be going back home, handing them their bus tickets. Dipper pleads to Stan that he can't give up, but Stan says that they've lost and heads out the door with Soos soon following him, telling him to reconsider. Dipper soon has had enough and tells Mabel that if Stan won't get the shack back from Gideon then they will have to do it themselves. Mabel also reminds Dipper that while Gideon may have the upper hand, they have one thing he doesn't have; journal 3 and the copying machine (though Mabel first states that her grappling hook is their advantage).
Dipper clones himself using the copying machine (although one clone jams and creates Paper Jam Dipper) and goes to attack Gideon. Gideon easily defeats the army of Dippers using water. As Paper Jam Dipper tries to hide behind Dipper, Dipper drops the third journal, causing Gideon to take the journal from him. Dipper tells Gideon to give the book back, but Gideon tells him that Dipper has no muscle, no brain, and is nothing without his book. He then waves them good-bye as tow of his body guards carry the twins away. After being dropped off in the forest Dipper realizes that it's over. A shocked Mabel tells him that he can't give up, as he always has a plan. Dipper dismisses it; the journal has the plan, and that the only courageous and cool thing he had ever done was because of the journal, without it he can't help anyone. With no option left, Dipper and Mabel head to the bus station and head out of town.
Back at the Mystery Shack, Gideon is overjoyed to have Dipper's journal and runs inside with it, but is stunned to find that it's Journal #3, as he thought there were only 2 journals. Thinking that Dipper dropped the third one to leave Gravity Falls with the first, he runs out the shack and asks Old Man McGucket if the giant Gideon-bot is ready, to which he suggests that Gideon might as well test it. Gideon gets into the bot and tries to get to Mabel and Dipper. Meanwhile at Soos' House, Stan has hit "rock bottom", having no friends, family, and being stuck on infomercials. He then looks at the Gideon pin, wondering how he was always one step ahead, eventually his hearing aid acts up and wonders what's causing it to happen. Stan soon realizes Gideon's weakness and leaves the house (stopping to kiss Soos' grandmother).
As the bus continues its drive, Dipper sees the bot and tells Mabel, and they run to the bus driver, soon realizing that Soos is the driver. Gideon chases them, and Soos, Dipper, and Mabel get cornered at the edge of a cliff. Mabel and Dipper escape and Gideon tells them he wants Journal #1. After Dipper tells him that 3 was the only journal he ever had, Gideon grabs Mabel and throws Dipper aside, claiming that he will rule Gravity Falls with Mabel as his queen. As Dipper steps back and remembers Gideon insulting him he sadly walks away, only to turn back, and he jumps off the cliff into the Gideon-bot. He and Gideon start to fight. Dipper eventually catches a punch, then starts to punch Gideon with Gideon's own fist.
Suddenly, the bot falls off the bridge and Mabel and Dipper are saved by Mabel's grappling hook. Gideon then lies to the crowd drawn to the sound of the crashing robot, saying that Mabel and Dipper tried to kill him by blowing up his bot using dynamite, and orders the cops to arrest them. As the cops get ready to arrest the twins, Stan shows up, revealing that the Gideon pins given to everyone at the Grand Closing were actually hidden video cameras, which Stan had deduced by realizing that his hearing aid had been picking up the feedback. The crowd shocked by this turn against Gideon and he is arrested. Stanford takes the deed and secretly 2, and he and the others return to the Mystery Shack.
The Fusionist's Lair II
The Fighters of Lapis ask what she is doing. Namine explains that they are not the people they are believing they are; in Fighters of Lapis 3 the originals had died. In this new timeline a mysterious man told her to plant the memories of the old Fighters of Lapis. Unfortunately, the mysterious man erased all of HER memories of his appearance and any identifying details.
The Fighters of Lapis suffer a brief identity crisis (except for the newer Fighters, who really don't care) just as the Fusionist finally reveals himself. They fight the Fusionist who attacks by fusing the environment and tries to trap characters in the fusing process.
The Fusionist is finally defeated, reversing any of the fusing processes he did. As Namine points out though, this is a new timeline and the events in MicroLapis haven't happened yet, so the world is still one and not the Fusionist's doing, despite what Ganondorf had said earlier.
Just then, the Castle That Never Was begins to collapse. Just then, Beetleworx Abomination appears. Created by the Fusionist, Beetleworx Abomination has been secretly analyzing and copying all of their moves. He can counter just about every move now.
After finally defeating the Beetleworx Abomination, his memory is erased and decides to join the Fighters of Lapis.
They return home, a little worse for wear.
They all returned to their home locations, obviously complementing the ramifications of this. Not only were they about to go through everything all over again, but some mysterious man was behind it. What did he have to benefit from this? How did he survive the black hole?
When they settle their things back in their room, Stanford checks on the kids. Dipper and Mabel tell Stan that they were talking, and they wanted to show Stan 3, exclaiming that they finally trust him.
Stanford laughs, crediting everything the twins told him to be a result of reading the book, and borrows it. Dipper starts to run after Stan to get 3 back, but Mabel stops him. Dipper and Mabel then agree to each other that Dipper does not need the book because he had defeated a giant robot with his bare hands. Afterwards, they go hang out with Soos.
Later that night, Stan takes the book and later opens the door behind the vending machine. He walks into a hidden laboratory and goes down an elevator to level 3. Revealing that he has Journal 1, he places the three books together with each opened at a specific page revealing the blueprint for a machine. He uses codes from the pages to activate the machine and pulls the lever to turn it on, he then says "Here we go" before the screen cuts out.
Genie urges Aladdin that he should use his third wish to regain his princeship, warning Aladdin that he has never seen a woman like Jasmine, but Aladdin, realizing that he cannot keep pretending to be something he is not, decides to keep his promise and wish for Genie's freedom. Seeing Jasmine's love for Aladdin, the Sultan changes the law to allow her to marry whomever she deems worthy. The newly free Genie leaves to explore the world while Aladdin and Jasmine celebrate their engagement.
Back on Earth, the elder Spock meets with his younger counterpart, who presumed the former to be his/their father. Young Spock is confused as to why his older self didn't come with Kirk and explain the situation. The older Spock states that he implied there may be universe-destroying paradoxes if Kirk told him the truth so that they would have to rely on each other, thus ensuring "a friendship that will define you both, in ways you can not yet realize." Young Spock asks if he was making a gambit; older Spock states that he made "an act of faith" to his old friend, which he hopes that he will show again in the future. However, younger Spock expresses his decision to resign from Starfleet to help rebuild the Vulcan race; older Spock points out that he can be in two places at once. He also advises his younger self in this case to put aside logic and do what feels right. The older Spock then raises his hand in the familiar Vulcan salute, and, feeling it would be inappropriate to say "live long and prosper" to himself, simply wishes his younger self "good luck."
Kirk is commended by Starfleet Command, promoted to captain, and given permanent command of the Enterprise. He relieves Pike, who has been promoted to admiral and is now recovering in a wheelchair. A proud Pike shakes his successor's hand and notes that his father, too, would be very proud of Kirk. As the older Spock leaves to help the remaining Vulcans establish a colony, Kirk, now dressed in the gold uniform of a captain, walks on to the Enterprise bridge. After he tells McCoy to "buckle up", and receives assurances from Uhura, Sulu, Chekov, and Scotty (who has barely finished talking to Kirk when he finds Keenser - now a member of his engineering staff - having climbed atop a console and orders him down) that their sections are ready to depart, the younger Spock returns to the Enterprise and asks Captain Kirk if he can be his first officer, offering to provide "character references". Kirk says it would be his honor.
As the Enterprise begins its journey, the voice of the elder Spock intones the famous motto that other starships named Enterprise have voyaged forward from:
Space... the final frontier. These are the voyages of the starship Enterprise. Her ongoing mission: to explore strange new worlds... to seek out new life forms and new civilizations... to boldly go where no one has gone before.