Scorpius is the half-Sebacean, half-Scarran Peacekeeper, and the primary antagonist of the series, relentlessly pursuing John Crichton for the secrets of wormhole technology locked in John Crichton's unconscious mind to create a wormhole weapon. He is the product of an experiment by the Scarrans - his Sebacean mother was raped by a Scarran in order to see if there would be any benefit to a hybrid. Raised by Scarrans, he has come to hate them, to reject his Scarran side, and to live for revenge against them. Both his physical attributes as well as his character traits are influenced by his race. Scorpius first appeared in "Nerve" and made his last appearance in "The Peacekeeper Wars Part 2". Being half Scarran, Scorpius' body produces an extreme amount of body heat, particularly when angry. However, being also half-Sebacean means that too much heat will kill him. To prevent this he wears a full-body cooling suit notable mostly for the interchangeable cooling rods contained inside his cranium that absorbs his excess body heat.

Scorpius prides himself on his patience and his intellect. Scorpius is willing to do absolutely anything to achieve his goals, which he is very honest about when it suits him. He will (and does over the course of the series) lie, kill in cold blood, order the deaths of multitudes, torture innocents, and sacrifice those close to him in order to get what he wants. He is also willing to aid his enemies or humiliate himself if it will further his goals. He has returned from supposedly fatal situations more than once, which he credits to his "foresight and preparation." He manipulates others to do his work but does much on his own; his obsession with Crichton and his wormhole secrets is proof of that. He is highly educated, very intelligent, and extremely clever. Only he knows how deep his schemes run and, while he claims his main desire is to eliminate the Scarran threat, protagonist John Crichton is loath to ever trust him.

His rank is never mentioned, and it is assumed that he does not officially hold one. Wayne Pygram seemed to confirm this during an interview on the Farscape DVD set,[citation needed] and Dominar Rygel XVI once claimed that he was "higher even than a captain" ("I-Yensch, You-Yensch"). His authority is not absolute, however, as Commandant Mele-On Grayza informed him when she superseded it. During the series, he is shown to have the authority to command a research base, a command carrier, a fleet of command carriers, and an even larger fleet in Farscape: The Peacekeeper Wars. However, the exact Peacekeeper ranks at this level have never been established in the show.