This movie is a follow up not sequel for Justice League: War and is also based on New 52 continuity.
Bruce Thomas (who voices Commissioner Gordon/Ubu) played the live action Batman in the short lived WB Series Birds of Prey as well as the OnStar Commercials that were airing at the time.
The film is loosely based on writer Grant Morrison's and Andy Kubert's Batman story arc titled Batman and Son. Although Deathstroke had no involvement in the story, the Joker did make an opening appearance and would not return until the infamous prose story which is said to have been an inspiration to Heath Ledger in creating his academy winning performance.
The story for which the film is based would serve as the beginning arc of writer Grant Morrison's epic run on the title. Morrison's story would run for seven years and progress across several titles, covering the Death of Batman arc, which lead directly into his Final Crisis and the rebooted Batman and Robin series. The newer title saw Dick Grayson taking up the cowl as Damian Wayne continued to serve as Robin throughout.
This is actually the second DC Universe Animated Original Movie to be based on writer Grant Morrison's work. The first which was a more faithful adaptation was based on his multiple award winning All-Star Superman book.