The lives of an ordinary suburban family change course forever when they discover their children have developed mutant powers. When the threat of a hostile government forces the family to go on the run to protect themselves, they join the ranks of an underground network of mutants. Together, the group fight to survive in a world where fear and misunderstanding put them at constant risk.
Reeva Payge purges the Inner Circle of those who disagree with her, leaving her completely in charge. Six months later, the Mutant Underground saves a girl from a Sentinel raid. Against the group's wishes, Eclipse and Caitlin meet with a criminal hacker to get info on the Inner Circle. Meanwhile, Polaris prepares for the birth of her baby.
Thunderbird contacts a mutant lawyer who recruited him to the Underground years ago, hoping she can help him find the Inner Circle. Lauren and Andy have a shared dream, which distracts Andy from his training and prompts Reeva to consider cutting her losses with him. Meanwhile, Reed must keep a huge secret from the group and Jace picks up the mutants' trail again.
The Inner Circle turns to an unexpected source for help when Polaris' baby suffers from a deadly illness. Meanwhile, Reed and Lauren take an excursion to deliver illegal meds, but Reed's powers complicate their plans. Then, Thunderbird and Blink meet the leader of the Morlocks - a shadowy group of mutants that live underground - who offers to help them find the Inner Circle.
The Struckers, minus Andy, begin to rebuild their broken trust, while Thunderbird, Blink and Eclipse visit Wire, hoping to convince him to help again. When they get there, they learn that something terrible has happened from Wire's brother, Graph. The team discovers that the Inner Circle is on the way to raid a mutant detention facility, so they make moves to try to intercept them. Meanwhile, Jace is contacted by a member of the Purifiers.
As Caitlin and Thunderbird struggle to save the life of a mutant injured in the Inner Circle's chaotic liberation of a psychiatric hospital, they discover clues to the identity of the powerful mutant Polaris and Andy were sent to retrieve. Meanwhile, as Jace joins up with the Purifiers to chase down the escaped mutants, he comes dangerously close to colliding once again with the Mutant Underground.
The Inner Circle prepares for a secret ambush, but Polaris is reluctant to join and Reeva tasks Esme with getting Polaris on board. Esme confides in Polaris, revealing her and her sisters' troublesome past. Meanwhile, Thunderbird trains Reed on controlling his powers and The Purifiers attack The Mutant Underground as they attempt to rescue a group of homeless mutants.
Reeva decides to announce her plans to acquire more funds for the Inner Circle; the Mutant Underground deals with Reed's powers and their instability; Jace meets a well-connected public figure who is in support of the Purifiers and their goals.
In attempts to stabilize Reed's powers, Reed, Caitlin and Lauren meet with Dr. Risman, a doctor who treats patients with debilitating X genes. However, Lauren finds out Dr. Risman is not who she thought she was. Following the Inner Circle's bank ambush, Thunderbird and Blink continue to work together to chase them down. Meanwhile, Polaris reflects on her troubled relationship with her father and takes steps to protect Dawn from the Inner Circle.
Tensions reach an apex within the Inner Circle while Andy defends Rebecca from Reeva; Lauren persuades Reed and Caitlin to destroy Dr. Risman's research; Jace works on a plan with the Purifiers; Blink and Thunderbird face their differences.
The Mutant Underground wrestles with the idea of recruiting the Inner Circle to assist them. Andy considers reconnecting with his family when he learns about his father's powers, but Lauren may not be as willing to have him back as their parents. Find out if the Mutant Underground and Inner Circle will be able to put their differences aside in order to save John from the Purifiers.
Reed worries as Lauren becomes intrigued by her ancestors and their violent powers. Lorna begins to reevaluate her trust in the Inner Circle after figuring out the past of Reeva's new trainees. Meanwhile, Benedict Ryan continues to encourage Jace to take action with the Purifiers. Marcos asks Clarice to go to the Morlocks in search of information on the Inner Circle and Thunderbird gets a call from Evangeline.
The nation is split more than ever and the dream of the X-Men nears failure while the Inner Circle and Purifiers rise in power; Evangeline plans to discuss reviving the Mutant Underground; Lauren and Andy are still unable to agree in their dreams.
Lauren stops sleeping so she can avoid the forces in her dreams pushing her towards joining Andy and giving in to her dark side. Glow is in trouble after being shot by the Purifiers, and Blink convinces the Morlocks to let Caitlin save Glow. Meanwhile, Polaris learns the details of what Reeva is planning, and Reed helps Lauren fight off her dreams.
Reeva increases the compound's security after an Inner Circle member disappears, but she later realizes that her plans may have been leaked; Caitlin and Reed aim to reduce Lauren's power with the serum in the hopes she can face her nightmares.
Lauren can't access her powers when it matters most, leaving Caitlin to take matters into her own hands when they are being pursued. Reeva finally reveals her plan for the Inner Circle and it's darker than anyone could have imagined. Meanwhile, Jace confronts some regrets about his actions and is torn between pressures from the Purifiers and his own beliefs.
Reeva prepares to carry out her plan for the Inner Circle, but not everyone is on the same page. Reed struggles to manage his powers and the family realizes that without enough of the serum, it's only a matter of time before he completely loses control. Frustrated and egged on by Benedict Ryan, Jace and the Purifiers are on the attack, but for Jace, things aren't as black and white as they once were.