According to the Sonic Adventure story arc, the Drakon Empire arrived on Mobius to retrieve the Chaos energy stolen by the ancient race of Echidna. The Drakons had produced this energy but had found it extremely unreliable. The echidnas harnessed this energy and stored inside their store of Emeralds, hiding it from the Drakons. The aliens made their way to Mobius to get them back, beginning the Great War. It seemed that the Echidnas won this war, but at a great cost.
After abandoning the planet, a Prosecutor returned to Mobius once he realised that the planet may once again be a threat. Doctor Robotnik had found a way to kidnap Flickies from the Drakon's home planet, through a Mobius Ring, in order to create a superior kind of Badnik. The Prosecutor was sent to crush any danger to their empire, seizing Robotnik and dragging him back to Planet Drak.
Thinking Robotnik was gone for good, Sonic the Hedgehog was surprised when he was accosted once again by his old enemy, allowing himself to be captured and taken to Drak. There, he was accused of destroying a Sentinel (from the story 'The Sentinel') and his only way to prove his innocence was to battle a particular prosecutor. In this case, Sonic was made to fight the new breed of Metallix. He only managed to prove his 'innocence' with the help of Tails, breaking up the fight and destroying the Knuckles Metallix with the help of a heavy door. With Sonic surviving the fight, the Mobians were allowed to return home.
Soon after, Emperor Ko-Dorr visited Robotnik on Mobius to fulfil a deal they made. In exchange for Drakon technology, Robotnik would lead Ko-Dorr to the Chaos Emeralds so that he could become the ultimate ruler of the Drakon Empire. In order to do this, Ko-Dorr unleashed a small army of Sentinels and a Prosecutor on Sonic and Tails, hoping to beat the location of the Emeralds out of him. The heroes easily managed to beat them, as well as saving the Emerald Hill Zone from The Master Sentinel. However, Grimer revealed to Ko-Dorr that he and Robotnik knew the Emeralds' location all along and vowed to help him retrieve them, disowning Robotnik.
Grimer led the Drakons to the Floating Island, where a large contingent of Prosecutors fought Sonic, along with the Guardian Robots, in the absence of Knuckles the Echidna. After the scientist found his way through the island's defences and revealed his identity to Sonic, he stole the Emeralds and placed them out of Sonic's reach. His plan wasn't over, as he moved to betray the Drakons and teleported them back to Drak. Straightaway, Grimer beamed Robotnik into the Emerald Chamber, having never really left his master. With the Drakons gone, Robotnik was free to absorb the power of the Emeralds.
The Drakons never returned to Mobius. They were seen some time later in Sonic's visit to the past. There, he witnessed the beginning of the Great War and showed the Echidnas how to defeat a Prosecutor.
Sonic the Comic Online
Although not directly related to the plans creator Nigel Kitching had for the Drakons, Sonic the Comic Online had the Drakons put a plan into motion that would put Mobius at their mercy. Sonic made his way back to Drak to plead for Master Scholar's help, the Drakon granting him a Chaos Tap. The mission went well, with Sonic defeating The Syndicate. However, the Drakons decided to invade Mobius, planting Robotnik as a puppet leader in charge of an army of Badniks.