During the G.I.Joe extraction of Destro and the Baroness from Destro's castle, Destro forced the castle to undergo a continuous and unstable transformation cycle. Megatron, sensing this from a long distance, was fooled into believing the castle was another Transformer, and flew up to investigate.
Upon his discovery that the castle was merely a man-made mechanism, Megatron was furious at having wasted his time travelling. Further insulted by Cobra Commander's offer of a deal, he launched an assault on the castle and its inhabitants. Despite a rapid response, Cobra weaponry was only minimally effective at best. Realizing this, Dr. Biggles- Jones commandeered a HISS tank mounted with the prototype railgun and fired it at Megatron, who was in gun mode.
The slug penetrated Megatron's body and continued into Earth orbit. Impressed, Megatron took possession of the tank and was about to dispose of the doctor when Cobra Commander appeared and informed him of her role as the weapon's inventor.
Megatron agreed to exchange excess technology from the Ark for the railgun and an upgrade of his body, supervised by Dr. Biggles-Jones. The upgrade was a success, and Megatron decided to honor his part of the deal, despite the fact that he knew the doctor had inserted a virus into the software that controlled the railgun (a virus which he found easily and removed just as easily). However, Biggles-Jones was actually a double-agent, and was able to leak information about Megatron's existence. The Joes managed to visually confirm this, and immediately contacted the Autobots about this.
Meanwhile, the Joes were discovered by Cobra troops and a large fight began. Megatron decided to take possession of Dr. Biggles-Jones as part of the deal, despite Cobra Commander's objections. A group of Autobots arrived to fight Megatron, but with his new body and weapons, they were slaughtered. Skydive managed to escape and with the help of G.I.Joe, snuck himself onboard the Ark. Spike Witwicky, the Headmaster component of Fortress Maximus, also got inside unnoticed.
Despite everyone's best efforts, Megatron clearly had the upper hand, and rather than see people dying in a futile effort to help her escape, Dr. Biggles-Jones surrendered herself willingly to Megatron.
Eventually, Spike joined with Fortress Maximus, and the two Autobots aboard the Ark attempted to stop Megatron and rescue Dr. Biggles-Jones. Realizing that the former Decepticon leader had simply become too powerful to beat one-on-one, Fortress Maximus ordered Skydive to leave with the doctor while he threw himself into the Ark's antimatter chamber. Skydive did indeed escape unharmed, and the doctor was delivered safely back to the Joes.