In New York City, Havok phones Elektra informing her that she was right and he couldn't kill Madelyne. Elektra tells Alex to come back home because Scotty's been real worried about him ever since he left. Elektra asks if he's going to have any problems getting away, because the Sentinels are still flying over the city scanning for mutants, but Alex assures her everything's fine. Alex tells Elektra to keep her eyes open, because Madelyne won't rest untill she's got Scotty and Alex won't let that happen. He also realizes that this city is hers and it won't be long before she decides to expand. Elektra says she always take procautions, that's why she's been hired to be the boy’s nanny in the first place. Elektra tells Alex to hold on because she hears something and goes check it out outside. Alex asks what it is, but she doesn't know.
Elektra tells Scotty to stay behind her and she prepares to attack as a huge spaceship appears. Elektra wants to go find Cerebro and cuts Alex off from the phone, and he starts to panic. Scotty tells Elektra that it's okay, because they are here. Three people step in front of the door and crush the phone.
Alex panics and starts running to the school, but the bystanders notice his behavior and as three Sentinels come, they recognize Alex as a mutant. Alex hasn't time for this and prepares to blast them, but more Sentinels come from the ground. Alex goes for the fight, but gets grabbed by two arms and dragged into the ground.
A short time later, Alex wakes up, and is greeted by Ben Grimm, the Thing from the former Fantastic Four, and his good friend, the Mole Man, plus Callisto and the Morlocks, and Ben welcomes Alex into the Underground!
In Washington, Reed has become President but questions his mistress, the Goblin Queen. She orders the Fallen to make Richards know his place. The Goblin Queen asks how their project is coming along, and Reed explains with an entire nation's resources at their disposal, things are working out faster then originally planned. Madelyne congratulates him and says she knew there was a reason she did not wipe his mind. She touches Reed and lifts him in a green telekinetic state, yelling at him there is no "we". She only keeps him around for the scientific problems.
Suddenly little vampires come running in from the window, and Bloodstorm coalesces. Bloodstorm explains that Havok has been spotted in New York and Madelyne, the Fallen and Bloodstorm decide to go after him, though she orders Richards to continue their project.
Back underground, the Thing explains that if there's going to be an organized resistance, it's going to start here. Callisto and the Mole Man have taken in both mutant and human alike underground to give them a saver place to live, which is a generous offer considering how they all turned their backs on the Morlocks during the Mutant Massacre, all of them but the Mole Man. The Thing explains that most surviving heroes survived through here and the Thing asks if Alex wants to be part of it. Havok asks who else survived since he heard most of the heroes died in the initial attack. The Thing apologizes for not entirely trusting him, but after all it was his wife who nearly killed him. Alex asks why he didn't let the Sentinels take him then, but Thing says that was Callisto's doing, because she's turning into a softy after she began dating the Mole Man.
They enter a huge place, where lots of houses are and the refugees are living. TheThing explains that the Sentinels and Havok didn't notice it, but a lot of people know there's something wrong and want out. The Sentinels have got this place sewn up tighter than anything else, but they've got their ways and their allies. The Thing hopes Havok is on their side and will help them out, but Havok wants to go to Westchester first. He gets a little angry but the Thing says he'll see what he can do for him. A little later the Thing takes Havok to a secret tunnel wich leads outside the city. It wasn't easy to convince the Mole Man and Callisto to let him use it, but they eventually agreed. Havok thanks him and promises he'll come back to help.
But then at the same time, the Goblin Queen, Ice-Man, Brute, Bloodstorm, the Fallen and some Sentinels arrive and prepare for a fight! Havok thinks the Thing sold him out, but it wasn't him, it was Callisto! The Goblin Queen explains she wanted her Morlock people safe and Madelyne manipulated her.
Madelyne asks Alex to just hand over Scotty, because then so much pain will be spared. Havok doesn't want to, of course, and the Goblin Queen hurts Callisto and orders the Fallen and the rest to take Alex and kill everyone else. The Thing and Havok team-up, but Ice-Man tells them they can't win from her, she's too strong. He thought he could, but failed and now he is happier then he has been in years and she can give him everything he wants, but Havok blasts him and says he doesn't want anything she can give him. The Thing fights Brute and Havok takes on Bloodstorm. He tries to get her back to herself, it works for a while, but Madelyne’s influence is too strong and Bloodstorm apologizes for attacking.
Alex blasts Bloodstorm who drops against the Fallen and they are defeated. The Goblin Queen congratulates him for defeating her group, and prepares to kill Havok. Suddenly the ground starts to shake and a huge hand comes out, separating Havok and theGoblin Queen from each other. It is the Mole Man and his aid. The Mole Man runs to his love Callisto, whose face is destroyed by the Goblin Queen now. Mole Man says it's okay and he'll always love and take care of her, no matter what. The Mole Man yells at the Goblin Queen that he'll kill her for this. The Goblin Queen laughs at his threats, and orders the Sentinels to step forward and kill them all.
The Sentinels step forward and prepare to attack, but get torn apart somehow. Everybody looks up and the Goblin Queen wonders what kind of magic this is. It's no magic, but simply the magnetic powers of... Magneto! Scotty has asked him to come get his father for him, and Magneto tends to keep his promises!