Despite WB Games Montreal being involved, in part, with Rocksteady’s Arkhamverse, Gotham Knights is in no way related. It’s an entirely new storyline crafted without the Arkham series.
The significance of that calls into question the existence of the Joker. It isn’t clear if he will appear in Gotham Knights. At the end of Arkham City, the Joker is dead—no tricks, no smokescreen. But since this is a different universe, it's a possibility.
Batman and the Joker have had years of history with one another, in one universe or another. The Joker practically lives for the Bat, a villain on the very end of the other spectrum.
Here’s the kicker, though: Bruce Wayne is dead in Gotham Knights. What purpose does the Joker have without his favorite vigilante to prod and torture? However, Joker does have history with the playable characters in Gotham Knights.
For example, in one story, Jason Todd is killed by the Joker. He’s later resurrected and dons the identity of Red Hood. Batgirl was paralyzed by the Joker, took on the persona Oracle, then healed and returned as Batgirl. He kidnapped Robin before, and frequently caused problems with Nightwing.
It would be interesting to see what the Joker would do. Perhaps Batman’s absence drives him crazy (crazier than usual), like how Bruce Wayne hallucinated the Joker in Arkham Knight. Maybe the Joker will find new vigor by toying with the Bat-family instead.
Just as equally interesting would be the lack of a Joker, and more of a focus on other villains. Creative director Patrick Redding has even expressed reasons for wanting to explore a different story during a panel at the DC FanDome:
Three villains have already been confirmed: Mr. Freeze, Penguin, and Talon. Penguin alone is a fantastic character
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