Alliance of Malice (working title) is the story mode for Malign Quarantine.
It begins in TOME, where Alpha and his allies are holding off a group of hackers. The hacker platoon is being led by Rockoon, who is quickly defeated by Alpha. After defeating Rockoon, Alpha sees a beacon-like portal and enters.
Alpha goes through the portal and finds Blake Belladona, who attacks him. After a brief battle, Alpha revives Blake's trophy when Homura teleports in. Homura warns the duo that a mysterious evil is coming to attack, using a mysterious virus whose effects are unknown. However, before Homura can finish explaining, Roman Torchwick and his White Fang army blast through and attack. The trio defeats him and set out to find more heroes before the virus effects them all.
Nergal Jr. wakes up in a strange room filled with 0's and 1's. Soon, he is surrounded by Glitch Drones and fights them off. As he traverses through the room, he meets Metal Sonic 3.0, batting him for a while. Metal 3.0 tells him that this is the Binary Chamber, where several worlds meet, and that he was sent by G.U.N. to find him and take him here. 3.0 then says they must find a portal to Skeleton Island, where they should find a mummy known as Chuck D. Head. Junior joins him on his mission, and the two look for the portal.
Mario wakes up and finds himself in the Internet, where trolls ambush him. After fighting off the trolls, Mario meets up with Inori, who knows an exit to the Internet. However, the exit is being blocked by a group of trolls. Things seem grim when suddenly, Death the Kid jumps down and defeats the trolls using his two guns. Mario, Inori, and Kid enter the portal that takes them out of the internet.
Neo Bowser Kingdom
Nergal Jr. and Metal Sonic 3.0 enter a portal, thinking it leads to Skeleton Island, but end up in Neo Bowser Kingdom, in an alternate timeline where Bowser destroyed the Mushroom Kingdom and now rules it with an iron fist. After being chased by an army of vicious Koopa Droids, the duo finds themselves in a Doctor's Office, where Dr. Mario is performing check-ups. Nergal Jr. and Metal Sonic 3.0 beg Dr. Mario to go back to his roots and "bust some koopas," as Nergal puts it, and Dr. Mario reluctantly agrees. The trio defeats the Koopa Droids and enters a portal to Skeleton Island.
Homura, Alpha, and Blake journey to the Forbidden Forest, where they find some White Fang soldiers, ready to attack them. After defeating the soldiers, Blake says she's going to contact her three teammates for assistance. However, Homura soon gets a vision of Madoka getting attacked by Virus Creatures, and runs off, leaving Alpha and Blake behind. At that very second, an army of monsters who have "abandoned their humanity" attacks the duo. Things seem bleak for the duo when a portal opens and Mario, Death the Kid, and Inori bust in. After defeating the monsters, Kid collects the Afreet Eggs that have once been the souls of the monsters. The group then sets out to find Homura.
Highway of Chaos
Nergal Jr., Metal Sonic 3.0, and Dr. Mario enter the downtown area of Neo Bowser City. They get trapped in an alley with Koopa Droids, but a bat-shaped weapon breezes past them, ripping off the droids' heads like LEGO minifigures. Batman 1966 flies in with his Batmobile, and the other three hop in. As Koopa Droids chase them down, Batman swerves through the streets of Bowser City until he reaches Bowser Tower. Batman, Nergal Jr., Metal 3.0, and Dr. Mario step in cautiously.