The New Batman Adventures never had a ‘proper’ climatic episode in the way that Superman: TAS and Justice League had, so I’ve considered an attempt at remedying that. My Batman Killing Joke edit (due out soon), is one possible elseworld take on that, but here I’m thinking of structuring a TV-length episode that can plug that gap.
To this end, you need to make use of the flashbacks from Batman Beyond: Return of the Joker and the prologue of The Killing Joke.
1. New Batman/Superman Adventures Intro
2. Begin with Tim’s capture
3. Flashbacks proceeds as normal until Joker dies and Tim breaks down
4. Switch to Killing Joke footage, Babs trying to talk to Bruce, Bruce cuts himself off, Babs almost loses it, quits being Batgirl, alter her narration to exclude a reference of ‘weeks’ passing
5. End with the pre-title scene of Batman Beyond Episode 1.