After
a cataclysmic event between the X-Men and the Brotherhood, both teams are gone
and harsh anti-mutant laws are in place which gave rise to the Mutant
Underground formed by Magneto’s daughter Polaris. She is captured while
rescuing her friends and later meets Reed Strucker who is a district attorney
with two mutant children Lauren and Andy. 
Andy
and Lauren are wanted by Sentinel Services for an incident at the school. Jace
Turner leads the operation however it drives the Struckers into the Mutant
Underground with Blink, Eclipse, and John Proudstar AKA Thunderbird. The
Struckers and the Mutant Underground work together to free Polaris and Reed
from Sentinel Services. Eclipse asks his old ex-lover Carmen the daughter of a drug cartel for help to rescue Polaris and Reed in exchange for future services. While rescuing them Thunderbird discovers an old friend Pulse who he left behind is brainwashed into working with Sentinel Services. Sentinel Services is determined to find the Mutant Underground. Reed Strucker discovers his grandfather and grandaunt were the terrorist twins known as Fenis. His father sterilize the X-Gene so he is no longer a mutant however the X-Gene still passed on to his children with the power of the Fenis twins. The team develops a risky plan to rescue mutants from Sentinel Services after one of them was used to spy on them. They use Lauren and Andy Strucker to take out the power station to cut electricity to the labs so Thunderbird and Eclipse and his team can free them. However Dreamer and the Fenis twins are caught which divides the Mutant Underground on what to do next.
One of the telepaths of the Mutant Underground uses the Struckers to orchestrate the escape of the mutants being experimented on. She is revealed to be one of the Stepford Cuckoos who works with the Hellfire Club and needs the Mutant Underground to take down the Sentinel Services Hound Program. The Stepford Cuckoos influence various members of the Mutant Underground to join them especially Lorna Dane, the daughter of Magneto who was a member of the Hellfire Club. The finale sees Polaris commit a terrorist act and some of the Mutant Underground joins the Hellfire Club.
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