IIRC Cyclops misses an entire hour of the movie after Xavier gets grabbed.
He's grabbed as well and reprogrammed by Stryker's son. I've read there were removed sequences in the storyboard where the fights against a controlled Xavier and Cyclops were extended.
All Cyclops does in this movie is:
- Be insecure about his relationship whenever Wolverine is around.
- Get sucker punched by Lady Deathstrike.
- Get mind controlled.
- Get clobbered by Jean while mind controlled.
Just a sad state of affairs. And mind you, this came out during Morrison's New X-Men run, when he was having the psychic affair with Emma, which means it was long after the Apocalypse possession. They could have made him interesting but the Wolverine money was too appealing.