Roots is a 4-part Sonic the Hedgehog story, beginning in Issue 135 of Sonic the Comic. It directly continues on from the previous story, Back in the Special Zone. This is also the last time Sonic sees the Chaotix Crew in the print STC.
After having been attacked by Blockhead Bill and Society Max, Sonic is understandably unenthusiastic when Vector the Crocodile shows him the Omni-Door, a portal designed to allow entry to the Special Zone whenever Sonic feels. Sonic reluctantly agrees to consult with Porker Lewis, leaving Charmy Bee happy that he can visit Mobius whenever he wants. Deep in the Mandrake Swamp, the evil being known as Root has located Blockhead Bill and calls to him using his mind. Visibly distressed by this call, Bill begins acting oddly, attacking his son Mighty the Armadillo, before throwing a Mandrake Root at Max, turning him into a dinosaur again. Mighty punches the beast through the wall of their headquarters. Outside, Bill punches Charmy, which sends him falling to the ground below. Fortunately, Sonic runs up the side of the tower and catches him. Mighty pulls his dad off the back of Max, which prompts Root to use a powerful spell - appearing in the sky and snatching Bill and Max.
On the flight to the Mandrake Swamp, Vector explains that everyone thought Root was just a legend, a story told to frighten people, but it has turned out to be true. In Root's ancient castle, Bill explains that he failed Root's orders because he thought he was fighting the Crimson Cobra, not Sonic. Root berates Bill further for failing a simple task of putting a chemical vial in New Tek City's water supply and reminds him he can shut down Bill's brain permanently. Outside, Sonic and Chaotix are on their way to rescue Mighty's dad when Vector gets stuck in some mud. When Mighty pulls him out, it seems as if a mud creature had hold of his legs and there's more of them. The fight against doesn't go well and ends when many spores put them all to sleep.
With everyone tied up, Root explains that everyone is going to work for him. Bill explains that when they were in the Mandrake Swamp, a couple of months ago, looking for Mandrake Roots and were captured. Root attaches a Mind Root to the heads of the Chaotix Crew, making them Root's slaves, but Sonic escapes from his chains, weakening them with sonic vibrations. Root nevertheless explains that Chaotix will take a chemical vial each and put it in the New Tek sewers, slowly changing the city into a swamp that Root will rule. A fight between Sonic and Chaotix breaks out, one that Sonic easily wins, but he escapes before anyone is seriously hurt.
Mighty is looking for Sonic, when Sonic emerges from his hiding spot and knocks him out. Sonic contemplates pulling the mind root from Mighty's neck but doesn't know if it'll kill him. Espio the Chameleon appears, having blended into this surroundings and hits Sonic, but Sonic is quick to fight back. Charmy dives at Sonic but is going too fast, sending him careering into some rubble. Despite a whack from Vector's tail, Sonic grabs some vines and wraps the crocodile up, turning him into a Christmas present. Finally, Bill and a dinosaur Max enter the fight, but Sonic wins by tickling Max into a laughing fit. Back in Root's room, Root shows off a display of power but Sonic, not impressed, kicks a pillar onto Root, crushing Root. A New Tek citizen, named Morton emerges from Root's body and points out the real Root - a small root running away. Sonic traps him in a handy jar, in time for Chaotix to return, their roots having dropped off. Morton reveals that Root attached to his body while he was exploring the swamp and somehow grew gradually all around him. Sonic suggests cooking Root in a bowl of chilli sauce with some rice.