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Trinity is the story mode for Crystal Warriors 2, which takes place shortly after Happy's defeat at the end of CW1's story.

Introduction

After the defeat of Happy in Fast-Food Chain From Another Dimension, Kyubey has assembled a greater team of villains to do his bidding. He has enlisted the White Fang to overrun many cities and kingdoms, while Junko Enoshima is preparing a weapon known as The Despair Missile. Raymond, Shovel Knight, Natsu, and Homura Akemi try to break into their base, and fight against an army of White Fang members. However, Monokuma appears and turns them all into trophies, taking them to the execution chamber. 

Mushroom Desert

Mario wakes up and finds that the Mushroom Kingdom has become a vast desert. Mario is unsure of why this happened, and encounters Sayaka and Mami. They say that a new enemy has risen, and the Crystal Warriors must reassemble to stop them. Monokuma then attacks the trio, saying that the Mushroom Desert was just stage one of his "Ultimate Despair Plan." Mario fights and defeats Monokuma with help from Mami and Sayaka. Pit flies in, with Monoeyes in pursuit. Mario and his allies defeat the Monoeyes, and Pit says that Palutena wants a word with them. 

High School of Despair

A young teenager by the name of Makoto Naegi is invited to the famed Hope's Peak Academy out of luck. However, upon entering, Makoto passes out and finds himself in a large auditorium with 14 other students, one of which being his childhood friend Sayaka Maizono. A monochrome bear emerges from a small podium, calling himself Monokuma. He claims that all the students are trapped in the building and the only way to escape is to murder a classmate and not be caught. A student by the name of Junko Enoshima taunts the bear, and she is impaled by several spears, seemingly on a whim. 

The remaining fourteen try to come up with a plan to escape. Chihiro Fujisaki tries hacking into the building's data banks, while Mondo Oowada picks up Monokuma and tosses him out of rage, causing Monokuma to explode. With Monokuma temporarily out of comission, Fujisaki is able to open a small chute for the others to escape. A copy of Monokuma generates and the students don't have much time, but Naegi manages to escape with Maizono, Toko Fukawa, and Leon Kuwata.

The Big City

Aiden Pierce is ordered by unknown associates to create a city-wide blackout, which he does so with ease. Nick Fury of S.H.I.E.L.D., not knowing Aiden's motives behind the blackout, sends Iron Man to stop him. Iron Man and Aiden fight, ending with S.H.I.E.L.D. arresting Aiden and Nick Fury using his phone to restore power to the city.

Meanwhile, Makoto Naegi and his group end up in the city and spot a black and white airship hovering over the city. This prompts Fukawa to faint, turning her into Genocider Syo. From the airship came a remote control, black and white Iron Man costume, and the group was barely able to defeat it. More duplicates of the suit come in, but Iron Man comes and stops them, telling the group to look for shelter. 

;Mech City

Hackers are running amuck at ;Mech City and AlphaFlamegirl, and Kirbopher are assigned to stop them. For every one hacker they stop, it seems like another dozen comes their way. Eventually, one of the hackers sends Alpha into a portal, leaving the other two to fight off the hackers. 

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