Teleportation is a dangerous tool in the hands of a capable adversary.
Thankfully for the Autobots, Skywarp is the only Decepticon known to possess that ability.
Depending on the timeline you follow, Unicron either recycled Skywarp into Cyclonus or Cyclonus's Armada.
Skywarp was stationed on Carob Island, where the Decepticons had set up a mining an construction operation.
Skywarp sat around with the other Decepticons listening to Megatron rant about his desire to steal energy from a power plant.
He was still there a little later when the Insecticons brought in the mind-controlled Grapple to analyze the plant, and took part in the battle that followed when the Autobots arrived to rescue their friend.
During the battle that followed, Optimus Prime seized Skywarp and Megatron and hurled them into orbit.
Skywarp was probably among the Decepticon Seekers who battled the Autobots over the captive Buster and Sparkplug Witwicky, and was also probably one of the Seekers who subsequently attacked Hoover Dam.
After the cerebro-shell controlling Grapple was removed, he turned on Megatron, and the Decepticon leader was sent crashing to several of his troops, including Skywarp.
Skywarp was among the Decepticons who went to stop Starscream and Rumble destroying a mysterious Autobot invention because Megatron believed the Decepticons could harness it.
When the Decepticons set out on patrol to seek the Autobots, Skywarp searched the skies over Earth's oceans, but had no luck.