Alpha Squad rushes to the Sentinel City Medical Center to confront the imposters posing as them. They face off against Malpractice, Inc. before finally confronting Doctor Migraine about the truth behind Sentinel City.

Having rescued Blue Streak, the Alpha Squad turns their attention to Doctor Migraine and the mysterious "LV". They soon discover a shocking secret that could literally change the world, just as some people who look very much like them show up on television...threatening to destroy everyone.

In an effort to restore Blue Streak's mind, Alpha Squad turns to Kid Titan's ex-girlfriend, Doctor Migraine's daughter Molly. In doing so they must venture into Blue Streak's subconscious and defeat the demons within.

The team must discover a way to unshrink themselves, deal with Bombshell's newfound godhood, and keep Johnny Legion's man bun in check. And this is all before they find out who is behind the murders in Sentinel City in the ultimate betrayal.

Having escaped from The Program, the pilots find themselves in the employ of The Founders. With more questions than answers and sent back to a previous metaverse, the team finds that trouble comes in all sizes.