Let go of the time loops.
There's no "proof" that Cassie was engineered by Weapon Plus. It's all inferred and you gotta fill in the blanks yourself.
Now as for the blanks, here's some copy/pasted posts from page 8 of this here thread.
i totally didn't think about Xorn's effect on Ernst/Cassandra. Magneto inadvertently reformed Xavier's dark side and the person who destroyed his dream in Genosha. my head is spinning.
Yeah, I was thinking just the other day about how Magneto never seems to know that one of his students is the creature who wiped out the mutants in Genosha, which is an event meant to trigger his violent attack on humanity, which in turn justifies the usage of the Weapon Plus super soldiers.
And there's my rationale for Cassandra being the genetic construct Weapon Eleven. Everything we think we know about her is memory implants and mutancies stolen from other mutants. She was released and programmed to inititiate the first phase of opening the Weapon Plus Super-Sentinel programme. Of which, she would most probably be the leader. She HATES them mutants!
what's really interesting about that is that once the plan is set in motion, it keeps going under its own inertia, even though it quite literally comes off the tracks in Paris.
- Cassie (Weapon XI) starts the ball rolling by attacking Genosha with Sentinels.
- Magneto is led into hiding and the whole Xorn ruse begins.
- Weapon XIV is sent to infiltrate the school, which simultaneously places them in a position to check Cassie before she goes too far with the Shi'ar.
- Weapons XII and XIII are being moved out of the World, presumably to get them in place to respond to Magneto's eventual attack.
however, Fantomex actively rebels. previous Weapons who were popped out into the real world (X, XI, possibly XIV) seem to have been memory-wiped first. Fantomex, crucially, was not, and he actively turns his knowledge of Weapon Plus against it. he manipulates X-Corp into destroying XII and freeing him.
the Super-Sentinels are supposed to be a team of Weapons XI-XV, but Fantomex has already taken himself and XII out of the picture, and he's gunning for XV. however, all the other parts are already in place and acting out their parts, so there's no real stopping it, since it doesn't seem like many of the pawns even know who they're really working for.
Fantomex, meanwhile, goes looking for Wolverine to recruit him for his little crusade against his creators. he starts to build a rapport with him until Logan's comfortable enough with him to take him up on his offer of going back to the World to destroy XV, which, ultimately, they succeed in doing. in the process, the dome of the World is cracked and the Weapon Plus satellite is destroyed. then Fantomex helps defeat Magneto, pre-empting the human retaliation.
I don't think that Cassandra being the "birth trauma" of Charles Xavier means that she can't also be Weapon 11. She certainly acts like she was one of Sublime's weapons, up to the part when the weapon ultimately turns against its master and is instrumental to his undoing. The Cuckoos, Fantomex/EVA, Ultimaton, and Wolverine all do their part.
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