In the aftermath of the battle, Shockwave accused Starscream of deliberately trying to foil his scheme by trying to steal Teletran 3. Starscream denied any treacherousness on his part, and Shockwave was just starting to come around when a recording Cobra Commander had programmed into Starscream began to play, informing the Decepticon leader of Starscream's general uselessness. At that point, Starscream promptly exploded, taking out the Decepticon headquarters in the process, courtesy of forty-five pounds of plastic explosives that Cobra Commander had lined his housing with, in case the Decepticon had ever escaped his clutches.
By the time Sunstorm tracked Starscream down once more, the Autobots had attached an energy siphon to the clone, severely weakening him. Sunstorm begged Starscream for his help, but Starscream refused by back-handing his "brother." Then, came bearing down on the both of them. Finding himself incapable of defeating this much bigger opponent alone, Starscream destroyed the energy-siphon attached to Sunstorm. The clone reawakened, and though Omega Supreme put up a good fight, Sunstorm defeated him using both his radiation powers and his guile. Starscream was then taken to a concealed mechanical door, which Sunstorm uncovered using his radiant powers. Claiming he was the "chosen one," Sunstorm ordered Starscream to open the seal. Starscream complied just as Jetfire and Bumblebee came bearing down upon them. Despite the Autobots' best efforts, they were unable to stop the Decepticons from entering the underground chamber, but soon caught up to them. Jetfire was able to quickly subdue Starscream, only to be left in a stand-off against Sunstorm, who held Bumblebee in his irradiated grip. Unexpectedly, Starscream turned on Sunstorm and used his recently-modified null-rays to blast his clone. After disabling Jetfire as well, Starscream kicked Sunstorm away, sending him tumbling down a nearby chasm.
The reactivated Starscream, along with his Seeker brothers Thundercracker and Skywarp, took a particular pleasure in dismantling the Autobot Minicars. When Megatron complained that he didn't rewire them so they could sit around and do nothing, Starscream playfully said they were only having some fun with their new "toys". Megatron ordered the three Decepticons to follow him, and when Skywarp asked Starscream what their leader's plan was this time, the air commander casually tossed 's head over his shoulder and said that he didn't care, as it was going to be evil, and evil is fun. Soon afterwards, the Autobots arrived and attacked. As Starscream attempted to choke , paid him back with a nice throat punch. All the combatants were then bombed by rogue members of the U.S. military.
With Megatron lost deep within the bowels of Cybertron, Starscream assumed command of the attack on the Autobot stronghold from the control room in the . Shockwave was less than thrilled to be taking command from him however, and claimed he would... "review the situation" once he had completed the taking of Iacon. Dismissing Shockwave's threat, Starscream had forcefully extract data from within to uncover the true extent of Megatron's plans. Uncovering information that would allow him to initiate the planet's mechaforming sub-structure, Starscream decided to activate it immediately to better allow him to "start fresh" with Cybertron. He instructed to carry this procedure out, hoping Megatron would be crushed in the planet's transformation sequence. Scrapper warned him against rushing the process, but Starscream simply didn't care about the Constructicon's misgivings. He gave Scrapper an ultimatum: he had a choice between beginning the mechaforming process immediately, or be himself be "mechaformed" by Starscream's enforcer, Motormaster. A group of Autobots were then discovered spying on the scene, and a firefight began between them and the Decepticons present. At this time, deep inside Cybertron, Optimus and Megatron were being fed visions of the future by the Matrix. In one of these visions, they saw Starscream participating in an attack on a hydro-electric dam on Earth. Meanwhile, in reality, Starscream continued to pressure Scrapper into activating Cybertron's engine, even as they came under heavy fire. Optimus, fresh from his victory against Megatron, soon joined the fight, and proceeded to beat down the bulk of the Decepticons stationed to guard the engines. With the odds turned against him, Starscream chose to flee, and the engines were destroyed after his departure.