Prime told his men to set camp while he went to seek the knowledge of the Underbase. Not that long after, Megatron came to the gates of Boltax as well. When Boltax's minions gave Megatron the same message about pain and suffering, Megatron responded with a grin on his face, "On the contrary, my dear disciples...we bring those gifts...to you!" The Decepticons immediately blasted them away.
Meanwhile, Prime met up with a robot in a room saying he was Boltax. The robot welcomed him, and Prime thanked him and started to speak, but was cut off by Boltax saying, "I know what you want. It is not mine to give." He then went on to say, "Within each Transformer is a core of knowledge called a database. Through that portal is something much more fundamental - a collection of knowledge that underlies all databases, much greater and broader in scope than anything in the universe. We call it the Underbase. What you seek is contained within. You may enter."
Nonetheless, Prime went in the Underbase and started to view its data. When Megatron walked in, Boltax said, "Please... you must turn back. I cannot allow you to pass." Megatron rammed his fist through Boltax's chest, saying "I didn't come to ask for you permission!" and threw him on the floor. Inside the Underbase, Optimus Prime noticed Megatron, who said ordered Optimus to cooperate, even offering to destroy him as "quickly and painlessly as [he] did Boltax"
Realizing the truth, Prime told Megatron that the entire mountain was Boltax, who had converted himself into a giant containment vessel to store the vast energies of the Underbase. He then added that he'd discovered that the knowledge contained in the Underbase was too much for any one Transformer to know, and that any attempt to input the Underbase would only lead to "madness.... and death"
Not believing him, Megatron ordered his Decepticons to fire at Prime. As Megatron started boasting about his victory, he didn't see Optimus get up and press a switch, which closed the flame vents, causing the energy inside to build up. Everyone got out just in time to see the Underbase being shot out into space. Prime lamented, "Cybertron's greatest treasure - gone all because I let pride and glory - not reason - dictate my actions. All because of me. I will live with this shame for the rest of my existence."
On present-day Earth, Ratbat, Soundwave and Starscream got hold of this Autobot information stored on tape. Ratbat and Starscream went into the Decepticons' "Realvision" and watched it, while their prisoner Buster Witwicky broke out of his prison and entered the Realvision. When the tape was done, Soundwave told Ratbat that the Underbase would be entering Earth's solar system in the next few weeks. Buster tried to escape the Decepticon base but was grabbed by Starscream after bumping into a wall.
Ratbat, wanting to take the Underbase for himself, told Starscream to dispose of Buster when they got to the Arctic. But when he did, he gave Buster the equipment to attract the attention of all the Autobots and Decepticons. While he convinced the Decepticons to fight each other, he escaped in Scorponok's ship to search for the Underbase. The Aerialbots found Buster and contacted the Autobots to come. And they did. Buster was placed in Fortress Maximus (who was being controlled by Spike Witwicky) to bring Buster's body heat up. Soon the Decepticons came and attacked. Fortress Maximus was knocked down by Apeface and Snapdragon. And soon after Blaster shot them off, Ratbat got on him!
In space, Starscream found the Underbase. The battle waged on the Arctic front. Ratbat somehow knocked open the compartment in Fortress Maximus and Buster fell out. Before Ratbat got the chance to kill Buster, Buster explained Starscream's plan, and that caused the Autobots and Decepticons to join forces. They took off in Ratbat's space shuttle to search for Starscream.
Meanwhile, Starscream started to absorb the powers of the Underbase but was shot out of the way by the Decepticon ship. But Starscream wasn't dead! He practically lifted Scorponok's ship and threw it and the Ratbat's! Starscream then said, "I go now to destroy the cities of New York, Tokyo, and Buenos Aires!" Optimus Prime knowing something like this would happen and had the Ark close by.
Once on the Ark, they decided they would go and meet Starscream on Earth and fight him. Blaster and Ratbat would go to New York. Scorponok and Grimlock would go to Tokyo. And Optimus Prime and Soundwave to Buenos Aires. Prime objected and told Fortress Maximus to go. They all left thinking Prime was a coward. But actually Prime was building a rocket that would reflect the Underbase and send it to Earth.
In New York, Starscream destroyed the Aerialbots, Jetfire, Bluestreak, Brawn, Gears, Goldbug, Mirage, Hoist, Hound, Jazz, the Seacons, and Blaster. Ratbat escaped, heading to the Ark, thinking Prime was going to use the Underbase for himself. In Tokyo, Starscream killed the Throttlebots, Thundercracker, Skywarp, the Dinobots, the Predacons, and Grimlock. Scorponok also left for the Ark, thinking Prime would use the Underbase for himself. In Buenos Aires, Starscream off-lined Laserbeak, Buzzsaw, Octane, Astrotrain, Blitzwing, the Technobots, the Terrorcons, Omega Supreme, and Soundwave. And before getting a chance to destroy Fortress Maximus, he heard a radio transmission and headed for the Ark.
Back on the Ark, Hi-Q (Prime's Powermaster component) and Buster launched the rocket. The rocket reflected the Underbase and made it go to Earth. At that point, Ratbat had taken Buster and Hi-Q hostage on the Ark, but Scorponok arrived, blasted everyone and went after the Underbase himself. Prime (with Hi-Q linked to him) stopped Scorponok just as the Underbase passed by.
Just then, Starscream flew up into the Underbase's path and absorbed the entire thing. He started to grow and mutate until he finally exploded, demolishing all that was the Underbase.