Part 2
Nightwing and Captain America can end up in an alternate universe when fighting some villain. There, they meet a different Batman, who is Thomas Wayne.
The villain that they are pursuing could escape back to the other world with a tentative alliance with the Joker.
Nightwing, Captain America, and Batman go back to their universe. They work hard and battle to defeat the villain.
While there, they could recoup in the Batcave, and this can be where Thomas meets Bruce, who goes downstairs after hearing some noise, maybe with Nightwing nursing an injury or Thomas doing this since he was a surgeon. This can be an emotional moment for both Waynes. Thomas could also maybe meet the other kids.
The Joker and the other villain can plan to reek havoc on Gotham and kill a ton of people. Bruce can end up helping by talking down his mother, who's fate is horriffying to him. Seeing her son, she kills the other villain after he tries to hurt Bruce. She also helps to stop the plan to save her son. This can end with her laughing insanely, but then crying with Bruce comforting her, kind of like Barbara did with Joker Jr. Tim in Batman Beyond, Return of the Joker.
There can be an emotional good bye from all of them. Before leaving, Thomas gives a letter to Bruce, like in the comics/tv show.