Scorponok is Megatron's second in command. The first thing we see him do is attack Dinobot when he challenged Megatron to a battle for leadership of the Predacons. However, no one seemed to take Scorponok seriously. He is both dumb and loyal to Megatron.
Like Tarantulas, Scorponok is a scientist, though is not quite as good at it as Tarantulas. He creates cyberviruses, one example being a virus he afflicted Optimus Primal with in an attempt to turn him into a coward, but instead it made him angry.
Scorponok is the rival of Terrorsaur, whom he disagrees with whenever Terrorsaur tries to take over as leader of the Predacons.
In the second episode, he fought Dinobot (who was now a Maximal) at a mountain full of Energon. In the episode "Dark Voyage", he blinded the maximals by blowing up some Energon.
In Episode 27, the Season 2 premier, "Aftermath", the quantum surge caused Scorponok to collide with Terrorsaur on his hover platform, and they both fell into the lava pit to their deaths.