Root of All Evil is a 2-part Double Sonic story beginn
Sonic the Hedgehog and Amy Rose are visiting the secret workshop of Tekno the Canary when they receive a message from Johnny Lightfoot. The rabbit says he's been fighting Badniks in other Zones so hasn't been able to see his friends, but assures Sonic that he doesn't need any help. Sonic suspects Doctor Robotnik is up to something and, sure enough, the Flickies' Island base sends out a call to Agent X, who insists that the mission to plant the Doom Seed underneath the Metropolis Zone is going as planned. Many metres above him, Gilbert Grumpy is spoiling the fun of two neighbouring children. Their football had accidentally gone over the fence and dented "32 blades of grass" in Grumpy's garden, leading to him confiscating their ball. The turtle emphasises that he likes his garden, proving slightly unbelievable when, seconds later, a massive weed shoots out of the lawn.
Tekno warns Sonic about the giant weed and, seconds later, the hedgehog turns up to rescue Grumpy. Sonic rips up the weed, even though Grumpy's more interested in the damage Sonic's doing to his lawn. Worse still, even more weeds crash through the soil, prompting Sonic to lock Grumpy in his own shed. In the city centre, weeds are shooting up everywhere, grabbing hold of citizens and even causing buildings to fall over. Amy and Tekno are attempting to solve the problem, but small weeds seem to emerge from the stem everytime one is destroyed. Robotnik looks on, commenting that the Freedom Fighters have got the "green" environment they always wanted. Sonic continues to save citizens while Amy (reluctantly) rescues Fabian Vane after his performance for a couple goes awry. Tekno suggests that the roots are all stemming from one seed (once Sonic stops interrupting her idea) and the three heroes head back to Grumpy's garden where everything started.
Sonic (again, reluctantly) frees Grumpy from his garden before Tekno uses a drill to dig the source of the problem. Despite an impatient Sonic stating he could get them there faster, the trio eventually make it underground and discover Agent X. The villain manages to escape before Sonic can catch him and the Doom Seed rears up, sensing danger. Tekno is captured and Sonic is knocked to the ground, so it's left to Amy to end things. Using a box of weedkiller taken from Grumpy's shed, Amy shoots at the Doom Seed, destroying it and all the weeds on the surface. Even Grumpy's happy, now that he can use the weeds as compost for his rose bushes. Everyone's happy except for Sonic, who still doesn't know Agent X's identity.
- Sonic is grumpy about still not knowing Agent X's true identity, despite this being their first meeting.
- Grumpy may be happy about the compost for his roses... but surely not the massive hole in his lawn dug by Tekno.
- Robotnik is correct that Sonic wanted a green environment (since the hedgehog stated so in the second part). Sonic should have probably been quite happy about this turn of events.
- Vane parodies Hey Jude by The Beatles, singing Hey Dude while two red setters contemplate marriage.