He lured Rodimus Prime, Ultra Magnus, Springer, and Arcee into a trap and transferred their minds to four tanks filled with formless synthetic protoplasm, which he ordered to be disposed of. The tanks were taken to a junkyard, where they were crushed. However, the synthoids had somehow taken human form and escaped seconds before their attempted destruction. They found a shack in the junkyard where four sets of clothes were hanging on a wall (although they were mysteriously already wearing some very long and complete undergarments; actually, in the Joe cartoon, the synthoids were created fully-clothed).
Meanwhile, Drath was preparing to scrap the Autobots' real bodies as well, but Snake persuaded him to save and utilize the now-mindless machines. Drath allowed his henchmen to take the Autobots for a small crime spree, during which the synthoid Springer managed to recapture his body and uncover Drath's plan to use the Autobots to blow up Autobot City. With Ultra Magnus's help, Springer stopped Drath from carrying out his plot, and the arms dealer and his cohorts were arrested. Snake, however, escaped capture.
A side note about synthoid technology: He may have been joking, but there was a moment when Springer looked at his reflection in a window and, rubbing his chin, remarked, "Terrific--I already need a shave!" The fact that the synthoid would *grow* hair suggests more than first meets the eye...do synthoids age? They convert from shapeless masses to human-looking adult bodies rather quickly, so how similar are they to real people? Unanswered questions...
There is one more shaky but interesting possible Joe crossover. Marissa Faireborne, of the Earth Defense Command, was once lured into a disguised Quintesson ship by a sort of holographic projection of her father. Her dad's voice sounded like the G.I. Joe code-named Flint (not that that's unusual--Cobra Commander sounds like Starscream). Interestingly enough, however, is that Flint's real name is Dashiell Faireborne...could he be her father? And where was Mom?
Some members of the G.I. Joe team were sent to guard Power Station Alpha, a compact, flight-capable nuclear power station that represented the best of human technology. Bumblebee was also watching it (although more covertly than the Joes), and he spotted the Insecticon Bombshell infiltrating the site in his tiny insect mode. Bombshell inserted a cerebro-shell in a nearby boy's brain and ordered him to walk in front of the moving Alpha. When Bumblebee transformed and saved the boy, the Joes saw him as a threat and destroyed him. Just then, the Aerialbots arrived and engaged in a brief battle, which ended when Superion received a radio message that Optimus Prime had died, and all Autobots were to return to the Ark.
Meanwhile, Bombshell had used the confusion to slip a cerebro-shell into Alpha's central computer, allowing him to control it and send it flying off to Decepticon headquarters. However, the Cobra scientist Dr. Mindbender used a strange and mysteriously handy helmet to override Bombshell's control and redirect the station's flight path. When Alpha arrived at Cobra Island, it was soon followed by Dirge and Bombshell, who feigned desire for alliance with Cobra. Cobra expressed a similarly insincere wish for friendship, going so far as to give Alpha back to the Decepticons (and giving them Dr. Mindbender as an emissary). The Decepticons, in turn, left Dirge to stay with Cobra, and he accompanied the terrorists as they attacked the Ark. Cobra, however, had learned of the Decepticons' plans to use Alpha to destroy the Earth and harness the energy released; therefore, during the battle, Cobra Emperor Serpentor used some sort of device in his jet to "jam Dirge's frequencies," preventing the Decepticon's weapons from firing. The energy build-up caused him to explode, thus removing him from the situation and allowing Serpentor to freely cease hostilities and ally with the Autobots.
The Joes, meanwhile, had run into G.B. Blackrock, the wealthy industrialist who had been aiding the Autobots. He explained the Transformers' situation, and the Joes tried as best they could to reassemble Bumblebee. They also joined the alliance with the Autobots and Cobra, and, with Ratchet's help, completely rebuilt Bumblebee into Goldbug.
While the airborne Autobots and Joe & Cobra jets fought a diversionary battle at the Decepticons' island base, the small team of Goldbug, Scarlett (G.I. Joe), and the Baroness (Cobra) secretly planted explosives on Alpha. Dr. Mindbender then used his helmet (which looked a little different this time) to regain control and launch the power station into orbit, where Cobra detonated the explosives with no one else's consent. After that point, the Autobot-Joe-Cobra alliance dissolved.
It was also discovered that Senator Barbara Larkin, the leader of the campaign to create Alpha, had sold out to Cobra in the beginning, ignoring safety problems and allowing the terrorists to steal it. She saw the economic benefits that the station's construction would bring to her home state, and, with the prospect of Cobra quicky and cleanly removing the hazard, she simply couldn't resist. However, when her deal was uncovered, she was killed by a Cobra assassin. She was the love interest of the Joe commander, Hawk, at the time, so he was very deeply affected.
The Joes and the Autobots appear to have gone their separate ways for quite a while, but their paths crossed again when Megatron appeared on Earth after the Unicron War. Starscream and Shockwave had stolen the Ark and taken it to the undefended Earth, not knowing that Megatron, Galvatron, and Ratchet were aboard. Ratchet caused the ship to crash again, and this time it landed in northern Canada. The local military investigated, but they were bested by the crazed Galvatron, who was later defeated by Fortress Maximus. Meanwhile, Megatron was able to repair and hide the Ark, which he used as a base for the next few years while he scouted for other Earth-bound Transformers. He thought he had found one in the European nation of Trans-Carpathia, but when he arrived, he discovered that it was only a castle which had been designed by Cobra's one-time ally Destro to convert between a rigid, functional design and a more romantic, Scottish appearance. Destro had been trying to escape from Cobra pursuers in the strange castle, so, in order to confuse them, he had set the transformation controls to a halfway point that caused the structure to continually reshape itself. Megatron arrived just as Destro escaped, and the Decepticon was outraged that he had been deceived by the human construct. When Cobra Commander, a mere human, suggested that they make a deal, Megatron flew into a rage.
Megatron attacked the castle, and the brilliant scientist Dr. Biggles-Jones (who was actually a spy for the U.S.) used her invention, the rail gun, against the Decepticon. Megatron was impressed by its power, considering it superior to his own fusion cannon. Thus, he reconsidered Cobra Commander's request to deal; he offered Cobra access to the Ark's technology if they would rebuild his damaged body and replace his cannon with a rail gun. Working from his specifications, Cobra made many changes to Megatron, such as giving him the ability to create a low-yield neutron implosion capable of destroying a starship. Megatron's new form also converted to a tank instead of a gun.
Megatron then took the Ark to Millville, a small town that Cobra had subjugated via a mind-control device. Megatron was seen there by a covert G.I. Joe team, so the Joes used a trans-dimensional warp communicator (given to them at some point by the Autobots) to contact Cybertron. Hot Spot, Chase, Brawn, Skydive, Override, and Steeljaw were sent to Earth, but it took some time for them to arrive because they were inexplicably using a ship instead of a space bridge or trans-time dimensional portal. In the meantime, the Joes attacked Millville, but Megatron ignored the conflict. He was only interested in Dr. Biggles-Jones, whom he considered valuable enough to take to Cybertron with him. However, for some reason he felt it necessary to remove the "excess flesh" from her nervous system and pack her brain in liquid hydrogen for the trip. He captured her and, against her protests, was about to core and freeze her when the Autobot strike team arrived.
Megatron stored Dr. Biggles-Jones in a compartment in his body, then engaged the Autobots in a battle that quickly cost the lives of Steeljaw and Chase. The other Autobots retreated and split up. Brawn went back to the ship, where Megatron found him. Using a neutron implosion, Megatron destroyed both Brawn and the spacecraft. When Megs returned to the Ark, Override attacked him in a suicide run that allowed the Joes to sneak the deactivated Skydive and Hot Spot past the ship's sensors. The Autobots automatically reactivated inside the Ark, and Hot Spot decided to leave and stop Cobra, to whom Megatron had given a truckload full of Cybertronian tech. Meanwhile, while Megs battled Override, Dr. Biggles-Jones escaped with the Joes and headed back to town. After destroying Override, Megs began pursuing the humans. Impressed by Override's bravery, Biggles-Jones decided to surrender herself to save her would-be rescuers. Megs returned to the Ark and left for Cybertron as Cobra Commander screamed about their deal; the devious Decepticon was aware of neither Skydive nor another stowaway, the human Spike Witwicky. Enthralled with Biggles-Jones's genius, Megatron decided to leave her body untouched. He also began rebuilding the damaged Starscream, but his plans threatened to come to an end when Skydive and Fortress Maximus (Spike's Headmaster partner) attacked him.
On Earth, Hot Spot fought Cobra and eventually destroyed their truckload of Cybertronian tech; however, he was injured and weary, and he knew that Cobra could overpower him. So, in order to prevent his own technology from falling into their hands, he destroyed himself. The battle on board the Ark ended similarly; while Skydive distracted Megatron, Fortress Maximus plunged himself into the ship's antimatter conversion chamber, vaporizing himself and setting off a chain reaction that blew up the ship. Skydive and Dr. Biggles-Jones escaped, but so did Megatron and Starscream.
Returning to Earth, Skydive served as the lone liaison between the Autobot army and the Joes; presumably, he was the one who notified Optimus Prime when Bludgeon began decimating the planet (incidentally, this is the point where the Joe and TF plotlines diverge; Bludgeon's carnage never occurred in the Joe comic).
There is one more interesting TF reference in the G.I. Joe comic. There is a brief scene in an obscure issue where a character is shown opening a nondescript box and removing a toy Megatron (which looks like the cartoon/comic version, not the real toy). It is presented as a gift, and the giver says, "His name is Jetfire, and he turns into a swing-wing fighter." The issue came out only two months after the original Joe-TF crossover ended. Also of note is that, in that crossover, we see a boy holding a Bumblebee toy (again, not looking like the real figure).