Disclaimer: Marvel owns all the rights to X-men. I do not own anything and if I did there would be a whole lot of things that would have been different in X3.
Jean knew what she had to do. Self preservation. Survival of the fittest. Weakness was not an option. Jean knew what she had to do. The Phoenix growing inside her knew what she had to do. Listening to the voices of her loved ones frantically trying to get the Blackbird to take off before the dam broke she made the decision. Sacrifice one to save many but not one-self. Not someone as powerful as she. You don't send the General of the Army to the front of the battle you send the private. The expendable but useful one.
Jean turned to Rogue and grabbed her face with her bare hands. Rogue's skin flared into action instantly absorbing Jean's powers. Rogue struggled desperately against Jean's strong grasp gripping her wrists trying to break free but to no avail. It was done. Jean's hands dropped from Rogue's face to her lap like dead weight. Emotionless and void of all that was Rogue she stood from her seat and exited the plane closing the door with a flick of her wrist. The sound caused Logan and Storm to turn around.
"What the hell was that?" asked Logan. Storm checked the system "The door."
"I realize that it was the door but why did it slam shut?" Storm turned to Logan "I have no clue why that door shut so don't give me any shit right now we have a major problem the damage to the Blackbird is too severe. The electronic equipment was fried when Magneto used his magnetic shield to stop us from crashing and the landing equipment is toast because Rogue crashed it. Scott try to see if you can override the landing gear mechanism so we can take off manually."
Before Scott can even do anything the Blackbird sprang to life. The engine hummed as the equipment repaired itself before their very eyes. "What the hell is going on? Wait…..The Blackbird is almost operational the equipment is aligning itself once again it is as if it was repairing itself. Now if we can just get her to levitate just a couple of feet than we will be able to get the hell out of here." As Storm was checking the rest of the equipment she yells over her shoulder "Jean do you think you can handle that?" There was no answer. Storm yelled again "Jean can you levitate the Blackbird a couple of feet off the ground!" Still no answer. "Jean why the hell are you not answering me!" Storm screams as she turns around. Storm sees Jean unconscious in her chair and gasps for air. Scott turns around and runs to Jean's side "Jean come on wake up. Come on baby answer me."
The Blackbird starts levitating off the ground. Logan scans the jet and realizes that someone is missing. He turns to Bobby and says "Where the hell is Rogue?" Bobby looks around "She was just here a minute ago I swear." The Professor closes his eyes and concentrates "Rogue's outside."
"What the hell do you mean she's outside?" The X-men run to the window Logan turns to Storm "You can't take off without Rogue open the door."
"Rogue's controlling the Blackbird she won't let me. She must of absorbed Jean to use her powers to fix the Blackbird."
Logan grabs Nightcrawler by the front of his shirt "You get her now." Nightcrawler disappears in a cloud of smoke only to return to the same spot. "I can't she is not allowing me to."
The Professor was still connected with Rogue says "It's better this way." Logan grabs the Professor "How the hell is this better?"
"Sacrifice one to save many."
"Damn it to hell Rogue get your Southern ass back on this jet you don't have to sacrifice yourself to save us."
"I'm sorry Logan this is the only way." With that Rogue broke the mental connection with the Professor and continued to concentrate to lift the Blackbird off the ground. A second later the a large piece of the dam broke and a wall of water broke through. Rogue lifted her hand up used her telekinesis to hold the water back.
Rogue called out to Jean and only Jean mentally "Why are you doing this to me?"
"This is the only way Rogue we wouldn't be in this mess if you did not crash the Blackbird."
"Then why not do let me do this of my own free will why are you controlling my body and my mind. Give me the chance to make the choice to help. I only wanted to help."
"Rogue you can't be trusted to make the right decision. I mean lets examine the evidence shall we you ran away from your home when your mutations manifested, you ran from the mansion because some boy told you to without even talking to any of the teachers or even the professor, you fall in love with a man who can't love you back because he is in love with me, you are currently dating a boy to forget said man who you cannot touch or be intimate with and who I might add is harboring feelings for our dear Kitty. Looking at your track record it seems to me that you are the queen of misjudgments. I think I am doing the world a service here by getting rid of a walking disaster like you."
"You are one sick twisted bitch. You are no better than Magneto using me so you can save yourself and make yourself out to be some sort of hero. Well listen to me Ms. Jean Grey when I'm done breaking free of you everyone will know just how sick you really are."
"Now little Rogue how would you propose to ever get the opportunity to do that if your role in this whole mess is as a martyr. Were you there when we covered martyrs in class? Let me give you a crash course they die for the cause just like you are about to right now. Good night sweetie."
With that Jean breaks the telepathic link with Rogue and uses her own telekinesis to break the whole dam wall to allow all the water to rush through.
Rogue uses the last of her strength to lift the Blackbird completely off the ground and out of the water's reach. A blue aura surrounds her as she struggles with the weight of the water. Jean glows red as she uses all her mental strength to will the movement of water towards Rogue.
Rogue closes her eyes to concentrate and hears a voice whispering in her ear "We need to rest child. Choose your battles."
Rogue releases her telekinetic hold on the water and allows it to surround her completely. The X-men collectively scream as they see their friend buried under the lake. The Wolverine howls as he destroys the interior of the Blackbird creating. The children start crying while Nightcrawler recites some Bible phrases to soothe the group. Bobby chants over and over "She's gone." Logan grabs him "Shut up you little shit! She's not gone. She's not gone." He breaks down letting Bobby go as he sinks to floor.
The Professor put his hand on his shoulder and instructs Storm and Scott to fly them home. Their victory turned bittersweet with the loss of a friend who sacrificed it all to save them. Scott was holding a crying Jean trying to consoler her. She turned her head to rest on Scott's shoulder while still looking at the lake and smiled her eyes glowing red.