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.
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 Struckers, minus Andy, begin to rebuild their broken trust, while Thunderbird, Blink and Eclipse visit Wire, hoping to convince him to help again. 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.
Polaris’ baby begins to suffer from a deadly illness, leaving the Inner Circle unable to heal her, and prompting them to turn to an unexpected source for help. 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, but the two factions may not have the same goals.
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, which, in turn, makes Andy second-guess his separation from his sister. Meanwhile, Reed must keep a huge secret from the group and Jace picks up the mutants’ trail again
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.
As the first season closes, Polaris learns more about her past and makes a crucial decision that could have impactful consequences. Meanwhile, the Mutant HQ comes under attack and, with everything to lose, relationships are put to the test and alliances shift.
Dr. Campbell attends an anti-mutant summit, attempting to take the Hound program national, and some of the team at Mutant HQ goes on a dangerous mission to stop his efforts.
As tensions heat up among the team at Mutant HQ, no one knows who they can trust. Fearing for his family’s safety, Reed rethinks their future at the compound. Meanwhile, Dr. Campbell proposes an improved program to Jace that could change everything.
At a moral crossroads, Jace is forced to hand over something valuable to Dr. Campbell. The team at Mutant HQ is divided on what they should do next, so Reed and Caitlin take matters into their own hands.