In 2049, the human population of Earth embarks on a migratory voyage to try to colonize other planets. They leave mechanical "orbots" to clean up the mess they made on Earth through littering and pollution. Raster, a high-level orbot who watches Earth through a planetwide computer network, is accidentally attached to a working nuclear missile by a lesser orbot and goes insane, becoming an evil dictator named Warhead. He declares himself ruler of Earth, and begins preparing to execute any humans who dare return to their planet.
Vectorman, a humble robot in charge of cleaning up toxic sludge by simply discharging it into the sun, As he lands on Earth after his last trip, and he finds chaos and confusion. Because all the other Orbots are controlled by Warhead (Vectorman having not been affected because he was away), Vectorman takes it upon himself to destroy the errant orbot and restore peace to Earth.
After saving Earth from Warhead in the previous game, Vectorman's sludge barge is targeted and destroyed by a missile. Vectorman escapes, parachuting down to the planet to battle with the Earth's multitudinous enemy; mutant insects. Now it is up to Vectorman to fight through the mutant bugs and find the most fearsome source infestation; the evil Black Widow Queen.