Sideswipe serves as an excellent Autobot Soldier during the War. Although, Sideswipe is one (of the many) to get too cocky in a situation. (e.g. Jazz)
Sideswipe accompanies Optimus and Bumblebee in the rescue of Zeta Prime in Kaon Prison. Along the way he and the others are imprisoned twice. The first time they are rescued from destruction in the nick of time by Air Raid who is subsequently captured. The second time is after Megatron takes notice of their infiltration and teleports them, without their weapons, directly to a cell. After escaping a second time, he and the others fight their way past Decepticon guards and release all of the Autobot prisoners including Air Raid, Jazz, and Arcee.
Eventually Sideswipe, Optimus, and Bumblebee make it to the cell where Zeta Prime is being held by Soundwave. After defeating Soundwave and his minions, a dying Zeta Prime is rescued and returned to the Autobot council.
Sideswipe appears in the Autobot HQ in Iacon (You can talk with him during that part of Optimus Prime's first level). He is shown commandeering a small Autobot ship that he uses to drop Jazz and Cliffjumper off at the Sea of Rust. After dropping the two 'bots off, he awaits in the sky. He then appears at the end of Jazz's level, swooping his ship down and saving the two Autobots from the deadly sandstorm. He does not appear again, and it is unknown where he went and what happened to him.