READ FIRST:
1. I'm Italian, sorry for not perfect english :P
2. This following story is based on deleted storyboards, Singer and Dougherty's interviews...
3. I'm a Marvel-fan and an X-Men fan. But i have accepted that the movies are adaptation of the comics and i like them. There are funny movies. The only one i really hate it's Ratner's X3.
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Bryan Singer and writers Michael Dougherty and Dan Harris are written on X3 on 2003-2004's period.
After that Singer, Dougherty and Harris left the project to join Dc Comics' Superman Returns. But before left the project, they have written an early draft of the screenplay and worked on an early pre-production of the movie.
During interviews, watching storyboard...I assume that the story plot of the canceled Singer's X3 was this:
"Several months after Jean Grey's death, X-Men are continuing their lives.
The only one who is still desperate is Scott Summers a.k.a. Cyclops. He thinks that the whole X-Men's team was so incapable because they aren't capable to save Jean's life.

Meanwhile Alkali Lake is dried up and in the sky appearing some lights. Charles Xavier and Magneto are known that Jeans has come back from death as a God-alike, a woman with the power of destruction, of a Dark Phoenix.
Jean was come back from the death with an aim: resolve mutants' affairs. No more X-Men, no more Brotherhood. No more fights. She's Phoenix now, she's above them.
Cyclops build the Danger Room and wants that all the X-Men are hardly trained. Wolverine is reclutant but Cyclops remember him that he's part of a team; Cyclops is now a leader and wants the best from the team. He wants that if a mutant will be in difficult, the X-Men can save him. Not like they can't with Jean.
The Cyclops' team it's compose by Storm, Wolverine, Iceman, Rogue, Kitty, Nightcrawler and Colossus.
Meanwhile Jean starts to make destruction in San Francisco.
She, also, destroy a ship because inside there are slave mutants.
Humans starts to thinks that mutants are a really menace but X-Men (Kitty here) are pursuing them to change their minds.
- Now i don't know what is the whole story in the middle -
I know there is a Colossus vs. Juggernaut...
I Know that Singer wants Sigourney Weaver as Emma Frost, the White Queen. In his story Emma was old like Xavier and she's and old Xavier's girlfriend.
In the end Jean/Phoenix says that he will continue his mission until Scott forget her and leave her go away. Cyclops understand this and leave her memory go away.
Jean leave the Earth and says to X-men - and Cyclops - "I Will watch you".
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So, people what do u think?