The idea I had was based off that comic panel of Scott in his underwear all scarred up, and some excellent fanworks I’ve seen/read of Scott with a Y-scar from Sinister vivisecting him.
And the brainwave was that, when Charles “massaged” Scott’s memories, Scott no longer “sees” the scars associated with repressed memories. They’re still physically present on his body, but he just literally doesn’t notice them because he has no reason to think hey should be there. Other team members rarely see him with his clothes off, and if they do maybe there’s a sight psychic suggestion of “Nothing to see there” or else they just... don’t ask because it would be too awkward to ask about obviously traumatic injuries Scott never EVER refers to.
But then along comes Logan, who’s both socially abrasive and resistant to passive psychic suggestion, who sees Scott shirtless, maybe after a mission when he’s getting patched up, or in the showers, and just immediately starts demanding war stories.
Scott’s obliging, and is probably enjoying getting to be a bit of a badass in front of Logan for once, sharing how he’s gotten his many scars. Logan doesn’t notice at first that there’s any number of smallish scars Scott doesn’t remember, or claims not to notice. But then Logan asks about one of the big ones.
“And what about that one, bub?” Logan jabbed the Y-incision with his thumb.
“What, my sternum?” Scott asked
“Doesn’t seem like Magneto’s style,” Logan said, “Was it Purifiers? Military intelligence?”
“Logan, I don’t know what you’re asking me about,” Scott said exasperatedly.
At first Logan thinks Scott’s just refusing to talk about it, but won’t drop it because he wants to know who would do that to Scott and if it was Stryker or if there’s someone else Logan has to go gut for doing such a thing to his favorite glass canon. He figures out that Scott legit has no memory at all of being split open, no memory of any surgeries, he’s not even aware of the scar. Logan finally gets him stood in front of a mirror, Logan tracing over the scar with his finger, and Scott sees it. He remembers how he got it.
...aaaaaand I haven’t decided where it goes from there! He’s definitely has a flashback to Sinister, but what then? Does he get caught in a loop, remembering, crumbling, and forgetting? Does he stoically hold it together while the seams crack in his carefully constructed mind? Does he want Xavier to put the lid back on his mind, or does finding out 5 to 8 (depending on our canon) years of his adolescence were blotted out drive him away from the team? And of course in the middle of that is Logan as well, who has his own very strong opinions and experiences with memory loss, experimentation, and loss of autonomy, many of them contradictory! I just feel like the whole scenario could get deliciously, delightfully messy.