Timeline A is how the story begins, however it can only be two chapters long due to the fact you need to fail chapter 2.
Our story begins in 1988, as a young Peter Quill meets his dying mother. Shortly before her death, she asks Peter to take her hand, which he refuses until it is too late. Upset by the events, he runs away and is abducted by the Ravagers.
26 years later, Ronan emerges from the wreck and prepares to destroy Xandar, but Quill distracts him, allowing Drax and Rocket to destroy Ronan's warhammer. Quill grabs the freed Stone, and with Gamora, Drax, and Rocket sharing its burden, they use it to disintegrate Ronan.
In the aftermath, Quill tricks Yondu into taking a container supposedly containing the Stone, then gives the real Stone to the Nova Corps. As the Ravagers leave Xandar, Yondu remarks that it turned out well that they did not deliver Quill to his father per their contract. Quill's group, now known as the Guardians of the Galaxy, have their criminal records expunged, and Quill learns that he is only half-human, his father being part of an ancient, unknown species. Quill finally opens the last present he received from his mother: a cassette tape filled with her favorite songs. The Guardians leave in the rebuilt Milano along with a sapling cut from Groot.
Meanwhile, a group of Primids go through the ruins of the Collector's place and grab the Aether, another infinity stone and head back into Subspace.
Chapter 1: Tabuu Returns
The story begins as Mario wakes up in a small desolate room and opens the door to reveal outer space. He walks outside, revealing Earth in ruins. Homura is floating and looks at him in anger. A giant dragon, ridden by a mysterious blue person that looks similar to Tabuu, but isn't, swallows Mario whole, waking him up.
Mario heads outside, where he is greeted by Homura, Batman, and Luigi. They talk about the return of Tabuu and what to do about it, as the scene shifts to Tabuu going up into the abstract golden castle we saw at the end of the Space Crisis II.
Tabuu enters and meets two of the brotherhood named Taizo and Bosslady. Tabuu explains his relationship with the Fighters of Lapis as well as his goal to defeat them for once and all. Taizo and Bosslady agree to help him.
Mario, Homura, Batman, and Luigi begin recruiting new members, some of which include Bat & Visor, Wii Fit Trainer, and Blue Mary. Mario hears tales about a legendary tactician, who he finds. After creating your Robin, they join the team as well.
As the group sits down to eat lunch, a group consisting of Primids and Aurum appear. The Fighters of Lapis get up and prepare to fight.
After defeating the group, a visage of Tabuu, Taizo and Bosslady appear, saying they're planning to attack the docks, where Shantae, Aladdin, Korra, and Will Smith are located and openly mock the Fighters of Lapis.
Chapter 2: Battle at Sea
The Fighters of Lapis heads to the docks, where they find a fleet of Aurum and Primid ships heading towards Shantae and gang's ship. Robin suggests that they need to take the fleets down by getting on board them.
They get inside the ships and take out the Primids. As the ships begin to sink, more and more ships come into view. Chrom, Sonic, Tails, Knuckles, Mai Shiranui, and Bonne Jenet come to the ship, and the Avatar comes up with a plan to take out the ships using oil, while they take down the biggest ship. Homura trusts that the Avatar's plan will work and head towards the giant ship.
As they get to the ship, they encounter Greg commanding the ship. After battling him, the ships begin exploding. It's way too soon for them to be exploding. Fighters turn into trophies left and right, and Subspace and Aurum forces grab them and put them on ships. Luigi and Batman are grabbed and thrown into a portal. Mario and Homura, unaffected by what just what happened, realize they just basically lost.
Homura explains that she can reset the timeline, although there will be consequences for doing so. Realizing that they have no other choice but to reset, they do.