In the Decepticons version, Brawl dies off-screen
Brawl is the one main cast character in the Decepticons version whose fate is left ambiguous. Towards the end of the game, Construct-A-Con mentions that "Barricade and the others" have perished. "The others" implies more than one Decepticon has died other than Barricade, and cannot refer to just Blackout. And Construct-A-Con is certainly not referring to Starscream. This suggests that Brawl has been killed off-screen by the end of the game, possibly by Starscream after he got a hold of the AllSpark, or possibly Optimus Prime like in the game.- It can't be ruled out that Construct-A-Con simply assumed Brawl is dead. However, given that the Decepticons can and do communicate via radio throughout the game, it's possible, if not likely, that Construct-A-Con tried radioing in on Brawl off-screen, only to get no response.
In the Decepticons version, Ratchet dies off-screen
Ratchet, similar to Starscream, is a boss of the opposite faction who fights as a boss once and disappears. While it makes sense why Starscream would bail (especially if his betrayal takes place offscreen), this isn't really consistent with Ratchet's character, as he's a loyal autobot by all indication in both games. He also doesn't assist the remnants of Sector 7 when they're trying to shoot down Starscream and Megatron in the final level. Thus, it's likely Ratchet was killed by one of Megatron's troops during the battle in Tranquility.