after some reflection, i seem to remember thinking that i saw ss merge with the raptor fleet, i also seem to remember them shooting down a friendly raptor thinking it was SS. at the time in the theater the action was moving pretty fast so i thought maybe i was just seeing things.

They don't shoot down a friendly. I've seen the same sequence seven times now (Internet can be your friend, if you let it) and the exact sequence is Starscream coming up from behind, taking out a few Raptors, and transforms into plane mode, ahead of the rest of the pack. He is then shot, but transforms, and slows down his speed to let one of the other planes pass, slashing at it while it passes him. Then he transforms again, just around the corner of a building, and when he is a jet-fighter again, he is joined by 2 other Raptors, while over the radio, you can hear "Don't let him out of your sight". At this moment, there are 4 Jet-fighters in the air above Mission City: 1 Raptor ahead of the squad, who Starscream allowed to pass earlier; Starscream himself; The two other Raptors who came in from behind. Call them Skywarp and Thundercracker.

 

Next scene: Fire reigns down on Megatron.

Looks like I was right. Starscream did screwed Megatron.

"Right", I wouldn't say. It's pure speculation, after all. Unless it is specified in one of the sequels that Starscream turned coat on Megatron and shot him in the back, this all is merely our own interpretation. But, yeah, you're not the first to have come up with the idea.

I would assume that the raptors that fire upon megs are a different squad of raptors, not the ones fighting with Starscream... at least thats what i thought when i say that scene, would explain it all