Season 2 began after Old Town had been attacked and walled in by the Company. Dav had been taken prisoner by the Sixes to a lab on Arkyn.
The season followed three overall plot lines. The first was the history of the green plasma and the connection it has to the Sixes, Khlyen, Dutch, and Dav. The second plot was the Company's intentions for Old Town and the wall encompassing it and the citizens. The third was the relationship story of Johnny and Pawter as well as more background relating to the Royalty and Their position in the Quad.
The season starts with an action filled ep "Dutch and the Real Girl. We are introduced to a new character Clara played by Defiance's Stephanie Leonidas. With many one liners between Johnny Pree Dutch and Lucy, the team moves from an outlaw Casino to rescuing Dav from the lab. We also learn that Dav has an immunity to the green plasma that controls the Sixes and that Khlyen may not be all bad.
The reunited team now sets plans on taking warrants that will aid in their investigation of the green plasma and the wall around Old Town. They return to Old Town to serve a warrant for the Company Officer in Charge Jelco. Season 2 will find him as one of the two enemies of our Killjoy team. Pree returns to what is left of his pub, and we also see Alvis return to the show.
Episodes 3 through 5 take the Killjoys on missions to discover the nature of the plasma. They find killer insects infected with the plasma in a mine on a rescue mission that results in failure. They do recognize that the plasma can cause a person infected with it to lose reality and judgment. Johnny does capture one of the giant centipedes to study and keep as a pet.
The fourth episode Takes the crew on another rescue mission involving children. We learn that the Company has a lab to experiment on the brightest children they can find in the Quad. Coupled with episode 5 we learn the Company has numerous experimental weapons in the works.
The fifth episode involves Pawter's return to her home. We learn why she had the falling out with her family as well as her return to the ruling elite. A destructive bioweapon appears in this ep resulting in a tragic ending.
Johnny returns to the crew but he now has a separate agenda from Dutch in that she is concerned with Khlyen, and he is going to help Pawter in her investigation of the Company.
The team travels to an Asteroid ship owned by a wanted mysterious collector in search of green plasma info. They do eventually find information that the plasma may be relating to an unknown invading force that has been around for centuries. Episode 6 has plenty of action humor and gives more detail on the strange relationship between Khlyen and Dutch.
Episodes seven and eight send Dutch Dav and Alvis to Arkyn while Johnny works with Pawter on the wall investigation. Johnny risks them all when he places his relationship with Pawter over the crew and is captured by Jelco. On Arkyn we learn that Dutch looks like a clone of Khlyen's evil daughter who battled the monk's hundreds of years ago on Arkyn.
In the closing episode, we lose two main characters. The wall is, in fact, a mind control weapon whereby the Company can alter the personalities of the citizens. The green plasma is exposed as a life form which is the basis of the invasion. The crew has some major victories suffers losses and sets their sights on a strategy to battle in season 3.