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Season 1. David Haller has spent his life being told he's schizophrenic. Locked up at Clockworks psychiatric hospital, he falls for Syd Barrett, a patient who can't stand being touched. When they kiss, they swap bodies, and Syd accidentally unleashes David's power: his friend Lenny dies trapped inside a wall. Division 3, a government agency, captures David, but a group of mutants rescues him and takes him to Summerland, run by Dr. Melanie Bird. With Ptonomy, Kerry and scientist Cary Loudermilk, she shows him he isn't sick: he's a hugely powerful telepath. The big discovery is that a parasite has lived in his head since he was a baby. It's Amahl Farouk, the Shadow King, who showed up as the dog King, the Devil with the Yellow Eyes and Lenny herself. When the team tries to pull him out, Farouk jumps from body to body and escapes inside Oliver Bird, Melanie's husband. At the end, a mysterious orb captures David.
Season 2. David returns a year later, thinking only a day has passed. Summerland now works with Division 3 and its chief, Clark, to stop Farouk from recovering his original body. A Syd from the future secretly appears and asks David to help Farouk, hinting that David himself will be the threat to the world. Farouk brings Lenny back in the body of Amy, David's sister, who dies in the process. Ptonomy dies too, and his mind ends up inside a computer.
In the desert, Farouk gets his body back, but David's allies have already decided he's the bigger danger. Syd confronts him: he tampered with her memory so she'd keep loving him. In front of everyone, David is treated as the villain. He escapes and takes Lenny with him.
Season 3. David now leads a cult in the desert, with Lenny at his side. He recruits Switch, a young woman who opens doors through time, and kidnaps Cary to boost her power. The plan is to go back and stop Farouk from infecting him as a baby. Along the way, David sees his parents: Charles Xavier and Gabrielle Haller. Every jump wakes the Time Eaters, creatures that devour time. Lenny, broken, takes her own life. David storms Division 3's airship, kills Clark and wipes Syd's mind, which is reborn on the astral plane and raised by Melanie and Oliver.
In the past, Syd tries to look after baby David, and David enters his father's mind to tell him everything. Switch, with help from her own father, takes control of the Time Eaters. The future Farouk talks with his younger self, and Charles and Farouk make peace. The ending is a fresh start: baby David will grow up with his parents, free of the parasite. Every character we know fades away, because a new timeline begins. David and Syd say goodbye, hoping their new selves will be happy.