The X-Men watch as anti-mutant protestors riot at the kidnapping of Senator Robert Kelly. Wolverine is furious that they saved his life only to be persecuted further. Professor X replies they must find Senator Kelly; and the first step in that is finding his captor Magneto.

Meanwhile, Magneto is holding Kelly captive on an abandoned tanker. Magneto explains the motivation behind Kelly’s abduction. He tells the Senator that they both agree a war is coming; but Magneto is willing to act to initiate this war. Growing up a Holocaust survivor Magneto realizes that there will be no peace between humans and mutants… until the mutants prevail. As he is about to kill Kelly, a sentinel hand removes the ceiling of the room.

Magneto repels the first two sentinels, but more keep coming. One apprehends Kelly and flies away. The others destroy Magneto’s boat and grievously injure Magneto.

Later the X-Men fly to the tanker aboard the Blackbird. They used Cerebro to locate Magneto. They find the ship junked and Kelly gone. Gambit is spooked when he finds the remains of a sentinel. Cyclops conjectures that sentinels saved Kelly. Rogue is surprised when she stumbles upon the hurt Magneto.

Elsewhere at an undisclosed location, Bolivar Trask is showing Senator Kelly the majesty of Mastermold. In addition, in return for his rescue, Track request that the Sentinels are placed in charge of mutant relations. Kelly agrees.

When Trask orders a sentinel to fly Kelly back to Washington DC, it refuses. Assuming the sentinel is defective, Trask tells Mastermold of the failure. Next, Mastermold reveals that the sentinels only follow his orders now; and h intends to replace Kelly’s –and other world leaders’ –brains with a computer. “It will be a vast improvement,” Mastermold announces.

Back at the Westchester Mansion, the X-men discuss their options. Magneto is still unconscious and too weak to question. They agree they must find the sentinels, but they do not know where to begin looking. Then Storm remembers that Gambit saw the head of the Sentinel program on Genosha. Professor X offers to scan his mind, and Gambit agrees as long as Xavier does not pry too much.

Inside Gambit’s mind, Xavier sees Bishop, Belladonna, Rogue, Mastermold, and finally Peter Gyrich—head of the federal security agency.

Later that evening in Washington DC, Gyrich frantically tries to contact Trask. He senses something is wrong. Suddenly the X-Men detain him after a brief chase that ends with Wolverine leaping off the Lincoln monument onto him. Just as Cyclops is about to question him, Gyrich’s communicator crackles, “Gyrich, it’s Trask! Mastermold is holding me prisoner!” Gyrich unhappily helps the X-Men with information but warns that Trask has made thousands of sentinels.

Having returned to their estate, the X-Men deliberate upon a direct assault against the sentinels. Gambit protests adamantly saying that it is a suicide mission. Magneto emerges heavily bandaged and agrees with the Cajun. Despite their arguments, the X-Men stand one by one and leave for the Blackbird. Gambit is the last to leave. As the Blackbird takes flight, Magneto muses from the ground, “The brave are always the first to die.”

The sentinels are prepared for the approaching attack. As Gambit, Wolverine, Jean, and Cyclops go underground to find Kelly; Storm, Rogue, and Jubilee prepare for an assault on terra firma. The sentinels appear quickly and en masse, and it quickly becomes obvious that Rogue, Jubilee, and Storm are gravely outnumbered—even with Professor X and the Blackbird’s cover fire.

Underground Gambit and Wolverine split up from Jean and Cyclops.

Storm’s team is in dire shape. A Sentinel incapacitates rogue, and the Blackbird is about to crash. Oddly, it begins to levitate. Magneto pronounces, “Did you really think I would let you die alone Xavier?”

Wolverine and Gambit are ambushed by a large group of sentinels. Self-sacrificially Wolverine tries to force Gambit behind two large steel doors that would separate him from the robots. Not one to avoid a fight, Gambit blows the door and joins his teammate.

Trask pleads with Mastermold to desist, that sentinels were created to protect humans from mutants. “Mutants are humans,” Mastermold observes. Jean and Cyclops attempt to rescue Kelly and Trask but are discovered by Mastermold. Mastermold stops them, but he cannot stop Trask from blowing up a nearby propane tank. The room explodes as Jean, Cyclops, and Senator Kelly narrowly escape. Jean leaves Kelly aboveground while Cyclops stays behind to look for Gambit and Wolverine. This time no one gets left behind.

Storm’s team is having far more success with Magneto’s help, but the sentinels all inexplicably retreat when Mastermold is in danger. Unexpectedly the nearby compound explodes (triggered by Trask’s actions). Magneto protects the X-Men near him with a force field, but Storm worries about her teammates still below. Rogue is primarily concerned about Gambit.

Underground Cyclops finds Wolverine and Gambit standing on top of a mound of vanquished sentinels. They beat a hasty departure. Above they are enthusiastically greeted—particularly Gambit who receives a kiss from Rogue, shielded by her hand of course.

Angrily Mastermold emerges form the rubble claiming to be indestructible. Professor X guides the Blackbird (filled with explosives and protected by Magneto’s force field) towards him. Right before contact, Xavier ejects himself; and Mastermold explodes.

Magneto bids his old friend adieu promising they will meet again.

Later Kelly reveals his new campaign platform. Not all mutants are evil, and many would use their powers for good.

Beast is shown in prison reading Shakespeare. He ahs received a presidential pardon (with a little nudging from a certain senator), and now he is finally released.

Taking some time for themselves, Scott and Jean enjoy a picnic. Unexpectedly Scott proposes. Jean is surprised but happily accepts. Little do they know someone Sinister is watching them.