Title: Danganronpa: Super High-School Level ShadowColts

Genre: Dark, Horror, Drama, Mystery, Crossover.

Crossover With: Danganronpa (story elements from both 1 & 2)

Premise:
A private school on a tropical resort island of Jabberwock called Hope's Peak Academy opens it’s doors to both Canterlot High and Crystal Prep Academy, revealing that they intend to study the interactions and bonding methods between students of different class. As such, the respective Principals of the schools choose their most promising students to take part in this program. With 12 selections from both schools, 24 students are sent to the island:

Canterlot High WonderColts:
Sunset Shimmer, Rainbow Dash, Pinkie Pie, Fluttershy, Applejack, Rarity, Derpy, Lyra Heartstrings, Bonbon (Sweetie Drops), Microchips, Sandalwood, & Flash Sentry.

Crystal Prep Academy Shadowbolts:
Indigo Zap, Lemon Zest, Sour Sweet, Sugarcoat, Sunny Flare, Twilight Sparkle (& Spike), Suri Polomare, Jet Set, Neon Lights, Pokey Pierce, Trenderhoof, & Upper Crust.

At first both teams of students can’t stand each other and plan to keep their distance...however Sunset notices this world’s Twilight acting weird and senses a strange type of magic not too far off. But the moment their boat get near the archipelago they all fall unconscious...

They soon wake up inside the school and are greeted by a sadistic teddy-bear named “Monokuma”, the self-proclaimed "Headmaster of Despair Academy", he states the instigator of their plight and gives the students two options: they can either live out the rest of their lives stuck forever on the islands, or they can attempt to escape by "graduating" through the only method… killing each other and getting away with it.

Suddenly a strange rabbit-like doll called “Usami” reveals herself as the “Class Teacher” and tries to stop Monokuma, the two exchange blows and end up perfectly matched. Usami reveals that she intends to make sure the students bond with each other and gain the "Fragments of Hope" needed to leave the island.

Sadly, things get even more complicated when Sunset and Twilight sense the magic again, and what’s worse: Bonbon & Pokey Pierce go missing, and even Monokuma is baffled by this turn of events! Leading to him striking a truce with his “little sister” until they figure out what’s going on.

Now the Shadowbolts and WonderColts must work together to not only find their friends but get off the island while avoiding Monokuma’s manipulations and trying not to go missing themselves. But who are the puppeteers pulling Monokuma & Usami’s strings? Will the opposing side really become desperate enough to kill to escape? Why did some of the students suddenly going missing? What secrets does this island hold? And what is the source the magic Sunset and Twilight sensed?