The guards are ready, but as Storm is about to open the door, Wolverine stops her. He says that he can smell gun oil and that there must be a load of armed guards in the next room. Rather than go with their original plan of going in quietly, Storm blows down the door and uses her power to scatter the guards.
The vehicles that Cyclops saw have entered the base and lots of troops start to run out. Cyclops tells Gambit and Rogue to attack them but try not to harm them -they just need to keep anyone else from entering the base. Inside the base, Morph tricks some guards into leaving the main control room so his teammates can enter. As they do, they set about destroying every mutant information file in the building.
Jubilee meanwhile has been taken to an old, run-down building in detroit. The building is, however, a hidden factory where Sentinel robots are being made. Gyrich wakes Jubilee up and wants to know more about the X-Men -he wants Jubilee to tell him who the most dangerous mutants are. He doesn't find out much and then Bolivar Trask walks in, the creator of the Sentinels. He wants to know why Gyrich has a mutant here and that they weren't going to strike against the mutants until 100 Sentinels were ready. Gyrich tells him to make the robots more quickly.
He then gets a phone call and learns that the Mutant Control Agency base is under attack. At the base, Morph destroys the last of the paper files as Beast deals with the computer versions be using a virus. With their mission complete, the X-Men re-group and then run out of the agency, back towards the Blackbird.
But as they approach the forest an army of Sentinels walk in! Wolverine runs up to attack the first one, not seeing that another has appeared nearby! Morph points it out and tells Wolverine to get back but sees that he is too late, so he runs forward to take the blast.
Back at the institute Jean suddenly cries out in pain. She was using Cerebro, the powerful mutant tracking computer, but says that she has lost all sense of Morph. Xavier then uses Cerebro but he also can't sense anything! This is kid-friendly terms telling us that Morph is dead. Later on, the Blackbird returns to the institute.
As the X-Men get off their plane, Wolverine punches Cyclops and tells him next time he'll use his claws. It looks like a fight is about to break out when Jean walks in and gets them to stop, but bad news is followed by bad new: not only has Morph died, but Beast has also been captured. Wolverine storms off and is about to leave the institute when he decides to make some improvements to Cyclops' car.
Wolverine then drives off and begins to think about what just happened. Morph had shoved him out of the way of the Sentinel and got himself killed in doing so. Beast also got blasted so badly he was sent several feet backwards and hit the electrified fence, putting him out of the battle.
The Sentinels kept coming so Wolverine went to fight them but got thrown out of the way. Cyclops and the others did a little better, managing to knock down or destroy some or the robots, but more and more of them kept coming. The X-Men re-grouped with Wolverine and made it to the Blackbird. Cyclops wanted to leave but Wolverine wanted to go back and at least try to rescue Beast. Not listening to Cyclops' protests, Wolverine started to walk back towards the agency...
...but Rogue used her powers to sap his energy, preventing him from going anywhere. As Wolverine stops thinking about the past he says he will avenge Morph. Meanwhile, Beast has been put in a cell and is hanging around on the ceiling, refusing to answer any of Gyrich's questions.
The President of the United States is seen making a speech the next day, saying how some renegade mutants attacked the agency, but they were stopped by the experimental Sentinel robots. Wolverine happens to be in a bar and tells them to turn the TV off, but the other people in the bar get annoyed with him and tell him to leave. He then reveals his claws and says that he goes wherever he wants to.
Cyclops then shows up and talks to Wolverine outside. He's kind of guessed that Wolverine wants revenge and asks if he is up for going to where the Sentinels are being made. At the White House, the President congratulates Gyrich on the Mutant Agency project but he is now to discontinue it with immediate effect. The reason being that the mutants who attacked the agency last night were willing to give their lives to destroy his files. She is wondering if they had good reason to be threatened? Gyrich leaves the room and throws away his papers. He then gets a phone call from Jubilee's foster father...
...who tells him that another mutant has come to their home. Cyclops is paying them a visit and is trying to find out more about Jubilee, he believes that she has been captured by Sentinels. As Martha explains this to her husband, he quickly tells Cyclops to get out -he's done something he shouldn't have and has told the bad guys that he is here. Cyclops complies and heads off, only to see a Sentinel heading his way. After showing how witty he is...
...he messes up the robot real good, doing enough damage to make it head back to base for repairs. The X-Men team climb aboard the Blackbird and chase after it. Back in Detroit, Gyrich tells Trask the terrible news: the agency project is no more and the Sentinel project may be the next thing to go. But he intends to take things into his own hands and reveals that they are going to take their operation overseas.
Just then the damaged Sentinel crashes through a window and lands on a generator, doing more damage to itself in the process. The generator is also damaged and the power to parts of the building briefly go down, giving Jubilee enough time to free herself and then blast down a wall.
But as she attempts to run out, a group of Sentinels surround her. All Jubilee wants to do is go home but as all hope seems lost, a voice tells her to duck as the Sentinels start getting trashed -the X-Men are here! Gyrich and Trask beat a hasty retreat as this time the team wipe out the robots with ease...
...and soon none are left. The next day, Jubilee has decided that she must go to the Xavier Institute as it is the best place for people like her. She tells her foster parents that they were the best and that she will come and visit them again.
She then leaves in a taxi. At the institute, Cyclops is still wondering if he did the right thing for Morph and Beast, but Jean tells him that he did what he had to do, and so did they. Jubilee arrives, rings the doorbell and enters the Xavier Institute.
The adventures of the X-Men are only just beginning!
Morph was only in the show just to get killed off -the writers wanted to show just how serious the show would be and killing a good guy off almost immediately was certainly one way of doing it.