A couple of weeks ago, /Film ran a podcast with X2 screenwriter Mike Dougherty, which touched on his treatment for X-Men 3 that got lost in the shuffle from director Bryan Singer to Matthew Vaughan to Brett ratner, though a few pieces still seem to have remained. And the chaps at First Showing have done the transcription duty.
Dougherty described his treatment, saying;
The idea – you open up with Alkali Lake but it's completely barren and dried up and there are these odd reports of strange phenomena going on around the world accompanied by bright lights in the sky.
The idea would be that both the X-Men and the Brotherhood realize that essentially a very god-like force had entered their reality and that it was causing disruptions around the world – mutant prisons being decimated. I had pitched an idea about a fleet of cargo ships getting torn apart in the Atlantic and you found out that they were shuttling mutants as slave labor.
So basically you found out was that Phoenix was going round the world taking things into her own hands and that she had basically returned as a god, which they did touch upon in X3. She had viewed herself as above the conflict, that she was here to end things on her terms, she was basically sick of the fighting and she was going to take things into her own hands and she didn't give a shit what the X-Men or the Brotherhood had to say about it.
And ultimately the way it was going to end, at least the version I was pushing for, would be that Phoenix was kind of like the Starchild at the end of 2001, she didn't just get stabbed and die again, but she kind of chose to leave.
The one idea that I loved, that I really wanted to do, was that Cyclops would build the Danger Room. Cyclops felt guilty, he felt that because the X-Men were too weak, they weren't strong enough, they weren't fast enough, that was the reason Jean died. If they were a little bit better at fighting, then she might still be alive. It was all about this guilt he had about her death and so he built the Danger Room to train them to be better. But in the end it really was about him not being able to let go of her, so that causes all the chaos and disruption in the movie. But in the end it's about him letting her go.
Ultimately she kind of becomes that cosmic force that Phoenix is known to be, she choose to leave Earth and become a god, or at least a higher level of intelligence, and she goes into the cosmos possibly to kick-start life somewhere else… The final scene for me would have been her telling Cyclops or her telling the X-Men 'I'll be watching.' Essentially she becomes a god.
Would it have been better? Maybe. Either way, I think I'd have liked the Ang Lee version more…