The first Rogue difference: Iceman's conversation with Professor X ends differently.
Iceman: "Someone that could take her power, take her place. She took yours once."
Professor X: "I'm sorry, Bobby, she must be dead. I haven't been able to make a connection with her for years."
Iceman: "That's because they're keeping her in the one place your mind can't reach from the outside. She's in Cerebro. She's in your house, Professor. They're experimenting on her. Trying to tap into her power, so they can take ours. Take all of ours."
Iceman: "We tried. It's too heavily guarded."
Iceman: "Kitty, I'm going to get help. I'm gonna bring back somebody to help you."
Xavier: "You do? Then, wherever you go, I will find you. And, Raven, if you make me, I will stop you."
Now the biggest difference after Xavier desperately said "She's in an airport, boarding a plane." regarding Mystique's whereabouts.
Xavier (after a little insight of a passport that fell on the ground): "Washington, D.C."
, this conversation ends differently and without an insight. Then a few additional scenes. Because of its extent, it has been marked as one coherent sequence.
First, Xavier adds: "She could be going anywhere."
Wolverine calms him down: "Get some rest, Charles. We'll track her in the morning and find out exactly where she's going."
A conversation between Hank and Wolverine follows.
Hank shyly comments his smoking: "You know that those things can give you cancer? I've done some toxicology tests in the lab, and..."
Wolverine: "You want something?"
Hank: "Yeah, I'm... I know it's complicated, and there's probably all kinds of rules and reasons for what you can and can't say, but I was wondering if you could tell me in the future, do I make it?"
Hank glooms and intents to leave: "Oh. Okay. It's okay. Thanks."
Wolverine: "Hey, kid? It's just the world I came from."
Now Hank alone in his room with several TVs running. Star Trek is on and one TV shows a report about Trask. Then he hears something outside and goes into that direction.
Shatner: "We're going backwards in time."
Host: "Tomorrow, in front of the White House, the President will make his announcement. He will be joined by Secretary of Defense Laird and has even sought the help of renowned scientist Bolivar Trask, his special advisor to combat this mutant issue. The White House has asked all three networks to air the event live, as it is a matter of importance not only to the United States, but to every citizen from around the globe. There are no other details about the event..."
Hank goes outside and runs into Mystique (not mutated at first resp. as Raven). He takes care of her and reveals how he feels during. She arouses and provokes him so much that he turns into Beast. After whispering sweet nothings on the ground, they talk about her ambivalent appearance.
Hank: "Raven... My God. I don't understand. What are you doing here?"
Raven: "I, uh... I guess, I just realized I have nowhere else to go."
Hank: "I've gotta wake Charles..."
Raven: "No, don't. Just wait."
Hank: "You really shouldn't walk on this."
Raven: "I've had worse. So, you've been living here all these years?"
Hank: "Someone had to take care of Charles. You know, he's missed you."
Raven: "He misses who I was. I'm not who he wants me to be anymore."
Hank: "I've missed you."
Raven: "So, you're like this all the time now."
Hank: "Like what?"
Hank: "No, not all the time. I take a shot in the morning, and I need another if I get worked up."
Raven: "Worked up?"
Hank: "Yeah, yeah, when I'm...emotional or excited. Any animal urges. Usually, I can fight them off."
Raven: "Well, maybe, we shouldn't have to fight off the things that come naturally to us."
They both mutate while kissing each other passionately.
Mystique: "Do you remember one of the last things you said to me? That I would never be deemed beautiful, looking like this? Do you still think that?"
Beast: "Maybe. You saw what happened in Paris. You know what they think of us."
Mystique: "What do you think?"
Beast: "I think you're beautiful."
Mystique: "What about yourself?"
Beast: "You should get some rest. I'm glad you're home.
Mystique: "Hank? Do you remember the last thing I said to you?"
Beast: "It was, 'Mutant and proud'."
Mystique remains alone.
And this is where it gets interesting because the old Magneto and Iceman now are on a rescue mission in Professor X's old house - and on a rotating basis, the scene with Magneto getting his head back (also in the Theatrical Version, please see 91:04-92:16 / 109:02-109:13) as a nice little montage. As a result, killing the guards happens simultaneously and while young Magneto reaches for his head, old Magneto subsequently unties Rogue.
What is one single scene in the Theatrical Version takes place step by step here and most of it is identical: only at the beginning, one gets to see young Magneto approaching the hub and when he takes off his glasses later on, there are two alternate takes. Screenshots only the different moments
of the altered scene. During the scenes with old Magneto, there are comments by Professor X in between every now and then.
By the way, it strike me as odd that after 10 years, Rogue is being examined on a stretcher at the very moment Magneto and Iceman break in. Even in the commentary, it is admitted that this is rather unlikely.
Professor X: "The old gas and water pipes lead straight to the house. The walls are made of reinforced steel."
Magneto: "In other words, a door."
Professor X: "You're walking directly over the hall now."
Going through a few more doors, the reach the inside while young Magneto is marching in as well - as already described.
To the scientists experimenting on Rogue, Magneto says "I've been on that slab. Let me show you how it feels." before he takes them out.
Still not moving, Iceman transfers some of his power to Rogue: "Rogue, Rogue, come on. Wake up. Wake up, it's me."
When she awakens, she sees Magneto first and Iceman calms her down: "Rogue, it's okay. He's with me. We're gonna get you out of here."
On the way back, the Sentinel army interferes resp. the Sentinels suddenly are in hot pursuit. Iceman tries to stop them but he gets killed in the process.
Professor X notices the danger: "Erik, Bobby. Get out of there! Now!"
Iceman uses his powers: "Take her!"
Rogue (while Iceman can't stop the Sentinel fire): "Bobby! No! Bobby!"
Eventually, he gets burned in a way similar to the Theatrical Version.
Magneto and Rogue keep running but one of the Sentinels comes really close and he sets the entire building on fire. Professor X watches from his ship with fear while Magneto and Rogue come aboard. When taking off, the Sentinel manages to reach the ship and it takes a few accelerations to give him the slip.
Rogue welcomes Professor X: "Professor!"
Magneto: "Get us out of here."
Professor X: "I know."
After a last shot of the burning interiors, we see Mystique (dressed up as Xavier) sneaking around in the quarters. She grabs the Cerebro helmet and destroys it with a little comment: "I'm sorry, Charles."
The rescue team lands and Rogue immediately displaces exhausted (and shaken by Iceman's death) Kitty.
Kitty: "Where's Bobby?
Rogue: "I'm sorry, Kitty."
Kitty collapses, Magneto gets her out after Rogue took over her powers.
Finally, Hank calls Wolverine and leads him and Xavier to the room in which Mystique left the broken helmet.
Rogue welcomes Wolverine: "Hello Logan."
Wolverine wakes up in the past and notices the new help: "Rogue..."
Hank comes in: "Raven was here. I screwed up."
Hank: "We can't track her now."
Xavier: "She's cut her ties."
Hank (after a little moment): "Hey, I saw in the news last night there's going to be an announcement in Washington this afternoon about a new protocol for mutants."