A good chunk of the movie is dedicated to rescuing Minho (Ki Hong Lee) from the clutches of the scientists in the powerful WCKD labs — including our old frenemy Teresa (Kaya Scodelario) — who are treating him and other immune kids like lab rats in the hope of siphoning off a cure to the zombifying Flare virus.
After their first wildly unbelievable train car heist fails to save him (with a few dozen other innocents sprung from harm instead as a consolation prize), they decide to storm the "Last City," a bona fide techno-fortress built to keep the uninfected population safe from the "cranks," and specifically designed to keep undesirables like Thomas (Dylan O'Brien), Newt (Thomas Brodie-Sangster), and Frypan (Dexter Darden) from getting in.
There's a big price to pay for getting through: they'll need to rely on the bitter, infection-riddled leader of a rogue group of insurgents that are lingering outside the wall, waiting for an opportunity to come in and wreck the place. And wreck it they do. With the help of Gally (Will Poulter), who's decided to be on Team Glader again, Thomas and friends infiltrate the wall through the tunnel system and make way to the WCKD lab building where Minho and others are being held. In return, Gally's boss Lawrence (Walton Goggins) basically gets the electronic keys to the city so he and his havoc-wreaking army can blow everything up just to spite those who've kept them out for so long. But skyscrapers and countless amounts of Last Citizens aren't the only ones lost in the fray.