Warnings: Unbeta'd, weirdness, mentions of experimentation, hinting at torture, did I mention the oddness of this?
Notes: I believe I can blame this all on the various bunnies and stories involving some Autobots either being flightless kin to Seekers, or actually Seekers who willingly reformatted for their own safety.
Disclaimer: No own no sue.
Red Alert actually remembered far more clearly then most of his fellow seekers in hiding, about those times when they were captured, grounded, and tucked away in that dark room until Shockwave needed one of them to study. He believed it was just the luck of being a junior medic and the only one who had any real medical training amongst those below and thus was kept more or less coherent and free of most cpu shattering experiments. It was easier to have him fixing and hoping he didn't mess up in the more complicated procedures, then to send a Decepticon medic to attempt dealing with the volatile seekers.
He still felt the echoes of the memory loops every now and then of desperately trying to keep someone online when their injuries had far outstripped his abilities, making him learn as he went to save them. Failure was common, and even his successes he worried about, as he could never truly tell if it did more harm then good in the long run. Curling up into a miserable ball in the corner of his cell and just wishing at times that someone like Evac or Crossline were there to help with their more experienced hands. The larger models he felt in his spark would have been able to fight back more when they came to take someone for the tests that would finally deactivate them.
It meant he was the first to learn through the various overheard conversations about the 'next step', being planned, and the fact that the pressure and threats of decimation had made their kind outside finally give in to Megatron's demands. At least the ones who did not freely join that is at the beginning. He still felt the horror and panic as freshly as back then when the first of their quickly diminishing numbers was taken away; and a strange mech was brought back. Until they actually ilooked/i and knew that this ground based mech was one of their own. He had been one of the last ones taken to be remodeled, thus he was in stasis when a rescue came. The story of a small group of Autobots stumbling upon the small lab by accident when looking for a rumored prison camp; though, if it was true or not they were not going to question it too much out of relief.
Even as they had to deal with the well known CMO who could see through the remodeling and began to try and unravel the programming that had been installed as a failsafe by Shockwave; to keep them from reversing the remodeling without any ill effects. By then the war was in full effect and it was too chaotic to proceed with regaining their old frames back, then Sentinel fell and a new Prime appeared. The chance to change back started to slip away, as by that time there were no true fliers on the Autobot side and it was considered just the way of the war. The ideas and conceptions of each faction too ingrained to be easily changed, not with how a great many things had been.
By now it was too much of a gamble to test that 'Autobot Code' and letting them find out there were Seekers among them.