He is permanently incapacitated in the final episode/issue of Borderline.
LARP & Comics Edit
The LARP and comics are almost identical, so Sovereign's (called Darkdeath in this incarnation) character is exactly the same.
In episode/issue 3, How to Train Your Tiger, Vijay, Joseph, and Thomas wander into a shed, revealing the Magic Maniac (Lucy) fighting against Sovereign. Sovereign kicks the Maniac in the head and Vijay almost unsheathes his sword, when he sees Darkdeath, revealing that it was his old friend, Bright Life.
Ever since, Sovereign had been in every episode/issue of season 1 as an antagonist. Sadly, most of these episodes/issues have been lost. One surviving episode/issue, Fury, which was the season 1 finale, which followed Darkdeath destroying Mighty School and the Ironic Warriors (now with Lucy) trying to stop him. In the end, Vijay and Lucy sacrificed their remaining power, and their lives, to destroy the villain. Darkdeath was weakened, but not killed, and chased the rest of the Warriors out of the city. Vijay and Lucy were each granted asylum in one of their friend's heads, Joseph and Marek respectively.
In the season 2 finale, Darkdeath wasn't killed, but stripped of his mortal form and sent away. How Darkdeath died or where he was sent away is unknown, as the season 2 finale was never finished.
In the upcoming Borderline books, which will most likely be written by Vee Kay Aech, Sovereign will be exactly the same as Darkdeath, simply with a different name.
Aech also states that he will "tie up any loose ends" and "fill in the blanks", implying that he hopes to write all missing issues as chapters/books.
In Legion of Legends: The Last Thing You See, Sovereign is promptly mentioned by the Man of Shadows to be, "the commander of my new army", most likely meaning that Sovereign was part of the Darkline. This may or may not be deemed canon by Vee Kay Aech and Lucy Deaton by the end of the book. Vee Kay Aech is currently suggesting to Deaton about bringing back Sovereign as a major plot point. Deaton will have to approve before this part of the story is written.
The first episode of The Ironic Warriors shows Sovereign and his brother, Ronan (who only exists in the WSU), attacking and raiding the Masterlands. In following episodes, Sovereign creates the Ironic Beasts.
Since the show will be written by the same person as the books, Borderline will most likely follow the same path for Sovereign that the books and comics have.