SPOILERS
Villains:
Joker - Killed off, which was shown in a flashback in Return of the Joker.
Harley Quinn - Reformed after Joker died, and is the grandmother of the Dee Dee twins. It's possible that the twins are actually Joker's granddaughters, as a scene in the comics, when Harley is talking to Black Canary, she admits to having a daughter whom she gave to her sister to raise since Joker was too busy with his "work" to be a proper father, and she couldn't bare to be away from her precious puddin'. This could be why the twins chose to follow Joker.
Talia and Ra's al Ghul - Talia sacrificed herself to allow her father to possess her body so he may live.
Clayface - Was implied to have been killed in an episode of Justice League (part of the Batman, Superman, etc continuity) after he was launched into space in a rocket, which exploded. He either died, or was blown to so many pieces that he could never reform.
Two-Face - Unknown. Was last seen in an episode of Batman where he completely snapped and developed a 3rd personality that may or may not have completely taken over both Two-Face and Harvey, or the 3 are constantly warring with each other in his head. He's likely still in Arkham as he no longer has the mental capacity to plan an escape.
Bane - Having lived on the Venom for so long, he's now immobile and living off a machine due to the Venom's side effects.
Mr. Freeze - He makes an appearance where he's seemingly returned to normal, but ends up reverting back. From what I remember, he dies at the end, or goes on the run. I don't remember, but I'm pretty sure he dies.
The Ventriloquist - The dummy is completely destroyed in an episode of Batman, but is seen somewhat restored in Batman's cave in Batman Beyond. The puppeteer was last seen making progress in rehab.
All other villains - Unknown. Were last seen arrested in Batman.
Heroes:
Batman/Bruce Wayne - Retired due to age. Is now Terry's mentor, assisting him from the Batcave.
Robin/Nightwing/Dick Grayson - Unknown, but is mentioned.
Robin/Tim Drake - Was captured and tortured into insanity by Joker and Harley, and implanted with a reprogramming chip containing Joker's personality, memories, and DNA, turning him into a Joker clone. Saved by Batman and Batgirl, but was no longer allowed to be Robin. Eventually settled down and started a family until the chip reactivated in Return of the Joker, turning him back into the Joker clone until Terry destroys it, restoring him to normal.
Batgirl/Barbara Gordon - Retired as Batgirl and now works as commissioner.
Alfred - Deceased. Mentioned only.
Catwoman/Selina Kyle - Her fate is unknown, but in an episode of Justice League (many years in the future) where Terry speaks to Bruce, he mentions that Selina "left" along with Dick and Barbara due to Bruce pushing everyone away. Some fans believe that she got pregnant with Bruce's child (Helena, who becomes grows up to become the hero Huntress), and so gave up being Catwoman, changed her name (to Irena Dubrovna), and fled Gotham to keep her daughter safe since people knew her identity.
Phantasm/Andrea Beaumont - Was revealed in an episode of Justice League (many years in the future) to be working for Amanda Waller. Was originally hired to kill Terry's parents to help shape his persona into one similar to Bruce's, but refused. Fate unknown after this.
Batwoman/Katherine Kane - Fate unknown. Was never mentioned outside of her movie.
Amanda Waller - Appeared in an episode of Justice League (many years in the future). Retired from her position. No longer at odd ends with Batman, and even admits the world needs a Batman. She helped shape Terry into who he is, even using DNA altering technology to make Terry biologically Bruce's son.
All other heroes - Fate unknown.
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