In the House of Magic on Planet Drak, Sister Haggra is showing her fellow leaders a vision, the Vapours of Destiny telling everyone that Sonic the Hedgehog is the one they seek. Master Scholar doesn't know who he is, feeling that someone of Sonic's type would not be interesting to his House of Knowledge. Haggra turns to Emperor Ko-Dorr who recently put an offworlder on trial. It was indeed Sonic but Ko-Dorr lies, saying the one he witnessed was much taller and 'more of a purple colour'. To throw off the scent, Ko-Dorr questions Haggra, but she angrily retorts that she wouldn't have asked anyone else if she knew who Sonic was. Master Scholar questions why they do not know who Sonic is, but Haggra is adamant that the Vapours are correct and Sonic will lead them to the Chaos Emeralds.
On Mobius, Sonic and Tails are defending the Emerald Hill Zone from yet another Badnik attack. Easily disposing of them, Sonic notices that the last of them is a camera and smashes it. Grimer is dejected, the Badniks having failed yet again. Doctor Robotnik, on the other hand, declares that the Badniks just serve as a reminder that he will one day rule the planet again. His plan is to create more of the Metallix Mark 3 robots along with the technology of Ko-Dorr to flatten Mobius. On cue, a Mobius Ring materialises in their Flickies' Island base and Ko-Dorr appears with several Sentinels to follow up on Robotnik's side of the deal. The Drakon reveals that he plans to use the Emeralds' power to take over the Houses of Magic and Knowledge and be the supreme ruler. Robotnik reminds him that the plan was for the Metallixes to get the Emeralds secretly, but the time for caution is over. In Emerald Hill, Sonic gets a warning shiver as the Floating Island comes into view, but there's surely nothing to worry about...
Suddenly, Sonic is attacked by a Sentinel, an intruder warned about by the Kintobor Computer. Ko-Dorr is jubilant, sure that Sonic couldn't stop one of his Sentinels. Robotnik tells Ko-Dorr not to get his hopes up, with Grimer reminiscing about their own failures. Grimer asks Robotnik why he's getting Ko-Dorr to capture Sonic for information on the Chaos Emeralds, but Robotnik has his own plan - to get the Chaos Emeralds for himself. As they discuss this, Ko-Dorr witnesses Sonic decapitate the Sentinel, so sends many more along with a Prosecutor. Tails worries that the Drakons may be invading, but Sonic is ready to stop the invasion dead. The heroes deal with the Drakons swiftly, able to unleash all their abilities in their home Zone. With all the Sentinels destroyed, the Prosecutor summons the ultimate challenge - The Master Sentinel. Back at Flickies' Island, Robotnik isn't so sure about Sonic's chances anymore.
Sonic isn't worried; nothing as big and slow as the Master Sentinel couldn't hope to stop him. However, its orders are to march towards the Emerald Hill village and destroy everything if Sonic doesn't surrender. As it sets off, Sonic throws a stone at the Master's back, enraging it into destroying a loop. Grimer isn't so sure Ko-Dorr will fall for Robotnik's plan, being too dangerous even for him. Sonic, at this time, is caught in the Sentinel's fist and certainly doesn't need Tails' help. He performs a twister move in mid-air before creating a Water Vortex in the river, surrounding the Sentinel. As Sonic jumps out of the water, the Sentinel seems to have been destroyed underwater. It seems Sonic is mistaken; as he warns the Prosecutor to stay away from Mobius, the Sentinel emerges and punches Sonic. Fortunately, a panel has been broken off of the Sentinel's suit, so Sonic gets Tails to lift him up there. Sonic then jumps inside and uses his speed to empty the suit of all its machinery. Powerless, the Sentinel crashes back into the river and the Prosecutor escapes.
At Flickies' Island, Ko-Dorr is furious and wants the Chaos Emeralds even more. Grimer decides to help him out, saying that Robotnik knew where the Chaos Emeralds were all along and decides to switch sides, preferring to work for the Drakons.
- The way Sonic disposed of the Master Sentinel mirrors his defeat of Mekanik in The Rampage of Mekanik.
- This story saw the only appearance of Sister Haggra and Master Scholar, although they return in Sonic the Comic Online story The Betrayal Of Mobius.
- 'Best of Enemies' is part of the Drakon story arc, sandwiched between The Evil Empire and Order & Chaos.