Furious at the turn of events, and suspecting they were on the wrong planet, Dinobot challenged Megatron to a duel. Instead, Megatron had Scorponok get rid of him, knocking him clear out of sight with a direct missile hit.
Not long after, Megatron and his Predacons battled the Maximals. With Cheetor's leg trapped under a rock and the Maximals scrambling to save him, the Predacons started to go into stasis lock, and had to transform into beast mode and retreat.
While Dinobot challenged Optimus Primal for leadership of the Maximals, the Predacons ambushed them, forcing Optimus Primal to save Dinobot's life. Stray fire from this battle revealed a huge energon deposit atop a mountain in the distance. Dinobot decided to join the Maximals and help them reach the energon first.
Despite efforts from both sides, the Maximals and Predacons reached the deposit more or less simultaneously. During the resulting fight, which had to be done in beast mode due to their proximity to the energon, Megatron bit into Primal's leg. Despite this, Primal was able to fight back effectively. In desperation, Megatron transformed and fired a missile at Optimus, even though he immediately locked up as a result. However, Dinobot knocked it out of the way with his tail, saving Primal but causing it to detonate the energon. Everyone survived, including Megatron.
When Cheetor accidently turned the Maximal and Predacon communications rooms into teleporter gateways, Megatron was about to destroy Cheetor when a Maximal bomb appeared through the gateway and locked to the Predacon ship. Deciding that survival was the better option, he released Cheetor long enough for him to disarm the bomb, then teleport away.
Not long after, an alien probe arrived at the planet and captured Optimus Primal. Megatron then targeted the Axalon, where the Maximals were trying to figure out who was going to be leader. During the attack, Megatron took on Dinobot who held his own and even appeared to be winning. After the battle, the Maximals went to free Optimus from the probe. Before they could do so, they were attacked once again by the Predacons. During the fight, Rhinox freed Optimus, who materialized out of thin air and took out all the Predacons by himself. Megatron and his men retreated.
Later, Terrorsaur found a floating mountian of energon that made him incredibly powerful. He challenged Megatron, who was unable to damage Terrorsaur and found himself literally blown to pieces. Terrorsaur's mountain was eventually destroyed by Rattrap, and was dismayed to find that in his absense, Scorponok had Megatron repaired. Megatron took back leadership of the Predacons.
When the stasis pod containing Tigatron fell from orbit, Megatron sent Waspinator and Terrorsaur to program the protoform into a Predacon. Desperate to get to the pod first, the Maximals bounced a message to the stasis pod off of one of the planets moons. When the Maximals and Predacons battled at the crash site, Megatron appeared and threatened to kill two nearby Siberian tigers. When the Maximals surrendered, Megatron was surprised to find that the stasis pod was empty; one of the tigers was in fact Tigatron, who helped the Maximals fight the Predacons. Realizing he had nothing to gain from the battle, Megatron retreated.
Salvaging a Maximal decoder chip, Megatron used it to both ambush the Maximals and to get to the next stasis pod first. This protoform became Blackarachnia. At this point, Terrorsaur brought in his "captive", Rattrap, who was pretending to help Terrorsaur out. While Megatron argued with Terrorsaur, Rattrap snuck up behind him and knocked him out with some sort of electrical stun weapon. Megatron was locked in a cage, but he soon got out using a voice override. However, instead of destroying Terrorsaur, he allowed him to lead the Predacons when the Maximals attacked their ship in an attempt to free Rattrap. As anticipated, Terrorsaur failed miserably, and Megatron used this opportunity to quel dissent among his troops.
Meanwhile, the Transformers on Cybertron had begun a search and rescue operation for the Maximals by sending probes to investigate diffrent times and places, including the planet the Maximals were currently on. Not wanting additional opposition on the planet, Megatron launched an offensive on the communications tower the Maximals were errecting. Despite the Maximals' best efforts, Megatron personally succeeded in destroying the tower before a signal could be sent out.
His emotions affected by Scorponok's malfunctioning Cyberbee, Optimus Primal broke into the Predacon base in search of an antidote. Megatron eventually lost the antidote to Primal, with Cheetor's help. After removing the Cyberbee, Primal attached it to the back of Megatron's neck and left before it exploded.
Completely by accident, Terrorsaur discovered a bug in the Predacon base. Using it to his advantage, Megatron had the Predacons pretend to turn on him and accidentally kill them themselves. Thinking the Predacons dead, the Maximals used parts from the Predacon ship to make the Axalon spaceworthy. About to launch, they were completely unprepared for the Predacon attack on them. With the other Predacons unable to get close enough to the Axalon as it was launching, Megatron leaped off a cliff and managed to hold on to an outcropping on the ship. Able to get inside, Megatron nearly succeeding in taking everyone out before Rhinox ejected him from the ship. During the fight, however, Megatron's pincer weapon became lodged into the ship's control console, causing them to crash (albeit softly). Rhinox stated that the ship would never be able to fly again.
Realizing how powerful and effective Rhinox was, Megatron had Tarantulas kidnap him, then used a device on him which would change him into a Predacon. The experiment succeeded far beyond his expectations. Rhinox became more aggressive, self-serving, and ruthless than ever before, even to the point of turning on the other Predacons so he could overthrow Megatron. When Rhinox's attacked caused Waspinator to blurt out that he was Shrapnel, Megatron was puzzled and had to be told by Blackarachnia who Shrapnel was. Unable to beat him in one-on-one combat, Megatron was forced to use his device to change Rhinox back into a Maximal. In the ensuing confusion, Megatron knocked Rhinox out, but was unable to terminate him due to timely Maximal interference. The machine was destroyed during the battle.
When Tigatron discovers a floating island using an alien weapon, Megatron sends Scorponok to keep an eye on Blackarachnia, whom he was beginning to mistrust. As it turns out, his suspicions were confirmed, but Blackarachnia had forseen his reaction and doublecrossed Scorponok, sending him plunging into the surface far below. The island crashed into the planet's surface, at which point a communication pulse was sent from the island to one of the moons, and then relayed into space from there.
When the Predacons recover the next stasis pod, it turned out that the protoform inside was badly damaged and mentally unstable. He would eventually take on the form of an ant, call himself Inferno, and believe that Megatron was the queen ant.
In one of his better plans, Megatron coordinated an attack on the Axalon which allowed them to steal a device that protected the Maximals while in their ship. Although the Maximals began to exhibit symptoms of becoming more beast than robot, Tigatron intervened during the Predacon "hunt" and helped them merge the two sets of instincts. Nonetheless, Airazor retrieved the device from the Predacon base and had it reinstalled in the Axalon.
When the ghost of Starscream possessed Waspinator's body and offered to help against the Maximals, Megatron quickly believed his lies and welcomed him into their ranks. Apparently, Megatron was not familiar with Starscream's history, including how he died. Soon, Starscream exhibited signs of betrayal, but Blackarachnia and Primal were able to blast apart Waspinator's body with a massive energon detonation, expelling Starscream back into outer space.
On a hunch, Megatron sent Inferno to investigate a strange energy anomaly from the inside of a mountain. The anomaly turned out to be a golden disk that had alien inscriptions marked on it. Realizing what the inscriptions meant, Megatron quickly made a truce with the Maximals. Curious as to what the Predacons were up to, the Maximals tried to sneak Rattrap into the base, but were caught. However, Tigatron did succeed in breaking in, and discovered the existence of the disk. Megatron intentionally allowed him to escape so he could inform Optimus that the aliens who created the planet were coming. Not long after, an alien ship entered the system and captured Airazor. With Megatron's help, Rattrap and Optimus Primal got in and Optimus sends Airazor and Rattrap back out. Primal was captured and the aliens, who took the form of Unicron's head and told him that they planned to destroy the planet. Primal escaped.
In an attempt to escape the planet, Tarantulas and Blackarachnia pooled their resources and entered the Axalon to steal an intact stasis pod. Meanwhile, the Maximals needed to get something spaceborne to stop the artificial moon that was destroyed the planet. When the Maximals captured the Predacons, they realized that it was the solution they needed. Using the transwarp drive that Blackarachnia was planning to install, Primal launched himself into space, where he planned to trigger a self-destruct in the pod and then escape. However, Megatron had rigged the transwarp drive to give him control, which he did. Megatron allowed the drive to self-destruct, but did not allow the escape hatch to open. The pod exploded, destroying the artificial moon. Parts of Primal's body was seen amidst the wreckage.
After Optimus Primal's destruction, Megatron, along with Tarantulas, were mutated by the quantum surge into Transmetals. Now believing the Maximals to be weakened by the loss of their leader, Megatron attacked the Axalon with Waspinator, where he retrieved both Inferno and Blackarachnia. After his attack was thwarted by the remaining Maximals, he returned to his base to consider his plans.
When two stasis pods were discovered in Predacon territory, Megatron and Inferno left and recovered the pods, in which were Silverbolt and Quickstrike. Convincing the two to join the Predacons, Megatron then attacked Cheetor with his new troops, only to be stopped by Rattrap. Summoning all of his forces, Megatron then launched an all-out attack on the Axalon, only to be stopped by the resurrection of Optimus Primal and Silverbolt's defection.
Believing that the quantum surge would cause the Predacons to send a hit squad to finish him off, Megatron ordered his troops to construct a number of jamming towers in Predacon territory. Angered by Tarantulas's unknown plots, Megatron was ready to destroy the spider when he said that he was no longer under his command, but allowed him to live to stop the alien Vok when they returned to the planet.
With the second Golden Disk, Megatron successfully commandeered the Vok Metalhunter and nearly destroyed the Maximals, planning to take it back to Cybertron as trophy to the Predacon Alliance, but the alien ship exploded when the control chair was disabled.
When Dinobot returned to Predacons, Megatron ordered him to battle Quickstrike one-on-one as a test of loyalty. Insisting that Dinobot return the Cybertronian Golden Disk to him, Megatron fully planned to betray his new soldier once he had the disk in his possession, but though he recovered the disk, Dinobot rejoined the Maximals at the last moment, forcing Megatron to flee.
Realizing that he would need decisive numbers to win the Beast Wars, Megatron ordered Blackarachnia and Waspinator to recover a stasis pod containing the rogue Maximal experiment Protoform X, which he named Rampage. Realizing Rampage was hopelessly treacherous, Megatron removed his spark from his exostructure and placing it in a cage that causes the Predacon great pain when Megatron applies pressure on it.
As soon as he had calculated that the quantum surge would reach Cybertron, Megatron, with aid of the Golden Disk, attempted to exterminate early humanoids before they evolved into the people that would aid the Autobots in the Great War. After nearly destroying the valley where humanity originated, Megatron was finally stopped by Dinobot, who destroyed all of the Golden Disk save a small fragment.
When the quantum surge reached Cybertron, the Tripredacus Council sent Covert Agent Ravage, a rebuilt Decepticon, to destroy Megatron. Allying himself with the Maximals and with the help of Lieutenant Tarantulas, Megatron was captured. But, while in Ravage's custody, Megatron used the Golden Disk fragment to display message from the original Megatron. Upon the sight of his presumably long-dead commander, Ravage set Megatron free and the two worked together to attack the Axalon.
Unfortunately for the Predacons, Rattrap destroyed Ravage's ship and the Decepticon, and the other Maximals severely damaged Tarantulas, Quickstrike, and Rampage. Seeing that his plan to destroy the Maximals had been thwarted, Megatron traveled to volcano under which the Ark was stored, where he overpowered Silverbolt and forced Blackarachnia to deactivate Teletran-1 and allow him entry into the Ark.
Inside, he passed by the ancient Autobots and Decepticons until he found Optimus Prime and blasted his head open. Unfortunately, the Maximals arrived soon afterwards, and Blackarachnia, who was originally a Maximal protoform, activated the security systems, pinning Megatron down. When he recovered, he was forced to withdraw by Optimal Optimus, along with Inferno and Waspinator, but vowed to return.
Shortly thereafter, he was defeated by Optimal Optimus and ordered Rampage to destroy the Axalon before (presumably) he returned to his own ship. From then on, his main goal was reentering the Ark and altering history by destroying Optimus Prime so that the Decepticons would win the great war. One of his major victories was the recapture of the Maximal computer program Sentinel, which he installed in the Predacon ship.
Realizing he needed new troops to defeat the Maximals, Megatron engineered the Cyber-raptors to test his new Transmetal 2 technology, which he had gained from a captured alien device. With this technology and a stasis pod, he created the new Dinobot, who was unswervingly loyal to him.
Megatron's determination to recapture the Ark led him to attempt several attacks on Blackarachnia, who had the access codes he needed to disarm Teletran-1. When she was undergoing the shell removal to transform her into a Maximal, Megatron dispatched Inferno, Quickstrike, Tarantulas, and Rampage to stop the Maximal efforts. Even though the attempt failed, he still had a backup plan with Tarantulas's help.
During a battle between Waspinator and Silverbolt, Optimal Optimus was drawn out, allowing Tarantulas to install a device that would allow Quickstrike to control Optimus's body through a special exo-suit. Knowing that Blackarachnia had downloaded the codes to Optimus, Megatron used him to capture all the Maximals except Depth Charge and imprison them. Entering the Ark, he found the original Megatron and procured his spark, merging it with his own. But Quickstrike was in league with Tarantulas and betrayed him, dropping him in a lava pit.
But Megatron was mutated into a gigantic dragon and, after nearly destroying Tarantulas, all but defeated Optimal Optimus, only to have his efforts cut short by the arrival of the other Maximals. He was last seen flying out of the Ark volcano and vowing vengeance to the Maximals who had deprived him of victory.