"Epilogue" is the second season finale of Justice League Unlimited. In addition, this episode also tied together and continued some plot points from Batman Beyond. This episode focuses around Batman, revealing a dark secret.
65 years from now: Terry McGinnis (now in his early 30s) breaks into the high-security home of Amanda Waller (now a very old woman in her 90s). He confronts her and demands answers. She seems unsurprised to see him, and insists on telling the story at her own pace.
Months earlier, when Bruce (now in his 90s) was suffering kidney failure and needed a tissue donor to clone new organs, Terry was tested and found to be perfectly compatible. Surprised, Terry had his DNA checked and was found to be Bruce's genetic son.
Terry is at first angry, believing that Bruce masterminded the whole thing in order to ensure that he had a successor. In his mind, Terry imagines himself storming into the Batcave and confronting Bruce, who doesn't deny the accusation and insists that the world will always need a Batman. Terry also imagines himself breaking up with Dana, whom he has continued dating since high school and now knows his secret identity and withdrawing from the JLU, saying "Batman is dead".
To prove he's wrong about Bruce, Waller tells Terry a story of a crisis that occurred before he was born:
- Ace, the last member of the Royal Flush Gang, began causing havoc when her powers developed beyond causing hallucinations to being able to alter the fabric of reality itself. Waller warned the League that Ace was on the verge of dying from a brain aneurysm, and the resulting psychic backlash would cause massive destruction and loss of life.
- At some point, Cadmus retrieved a special weapon to kill her and prevent the disaster, which Batman volunteered to use. However, when he reached her, he wouldn't use the weapon. Instead, he asked Ace to reverse the changes she had made, and comforted her over her lost childhood. With him by her side, she died peacefully, and the world returned to normal.
Waller tells Terry the truth: she was the mastermind, not Bruce. After the Cadmus Crisis, Waller went from being the Justice League's chief antagonist to its ally. In her role as the Government Liaison to the League, she came to know Batman very well, gaining a great deal of respect for him. She also met a lot of interesting people but none of them were comparable to Batman as he saved the day using his wits, body and will (as a post to others and their gained superpowers).
The incident with Ace demonstrated to Waller that Batman's greatest attributes were his compassion, and his iron refusal to never take a life. But as time went on, Waller saw him age, and realized he wouldn't be around forever or might eventually be killed. However, in her mind, the world needed a Batman.
Waller used her old Project Cadmus contacts to launch "Project Batman Beyond". Bruce's DNA was obtained years previously during one of his exploits. She found a young couple, Warren and Mary McGinnis, that was almost an identical psychological match for Dr. Thomas and Martha Wayne. When Warren went in for what he thought was a flu shot, his reproductive DNA was overwritten by that of Bruce Wayne's by nanobots. A year later, Terry was born, genetically the son of Mary McGinnis and Bruce Wayne.
Genetics, however, do not alone make a Batman, so Waller hired an assassin to kill Terry's parents when he was eight years old as the three of them were leaving a movie theater showing The Grey Ghost Strikes hoping that the same tragedy would cause the same response. However, the assassin couldn't bring herself to kill them, as Batman would never resort to murder because it would destroy everything he stood for. Waller was forced to agree, and the project was effectively scrapped. With the McGinnises spared, Matt would be born.
Terry is not soothed, believing that, whether Bruce or Waller was the real mastermind, he is still "cursed", in that his identity of Batman was written before he was even born. Waller implies that she believes it was a form of divine intervention which led to the death of his father. Why Terry became Batman was a mystery, but she still says he is free to choose his own path. He is Bruce's son, not his clone. In her assessment, Terry may not be as smart as the old Batman, but he is every bit as devoted to helping others—and, she adds, he could have worse role models than Bruce Wayne, who "for all that fierce exterior, I've never met anyone as dedicated to helping his fellow man... except maybe you".
In parting, she gives him some last advice: "You want to have a little better life than the old man's? Take care of the people who love you. Or don't. It's your choice".
Taking this advice to heart, Terry returns to the Wayne Manor, prepares to propose to Dana, shares a moment of mostly unspoken reconciliation with Bruce, and takes off to speak with Superman on a case.
In the skies of Gotham, something winged flies past a police hovercraft, causing one of the pilots to ask "Did you see that?"
- When questioning Bruce about the Cadmus procedure that could have altered his DNA, Bruce says that those procedures have been illegal for decades. Terry responds, "Didn't stop the Joker from using them on Tim Drake", referencing the Batman Beyond: Return of the Joker movie.
- Dana Tan and Terry have continued dating since high school throughout Batman Beyond, and she now knows his secret identity.
- The members of the JLU who appear in Terry's dream sequence—Kai-Ro, Warhawk, and Aquagirl—were introduced in the Batman Beyond episode "The Call". Warhawk likewise appeared in the previous Justice League Unlimited episodes, "The Once and Future Thing Part One: Weird Western Tales" and "The Once and Future Thing Part Two: Time, Warped", in the latter of which Kai-Ro was mentioned. The absence of Big Barda and Micron is unexplained; Superman does not appear, but Bruce mentions that he is still active.
- Likewise, the rogues who appear as members of the Iniquity Collective consist of three rogues from Batman Beyond: Inque, Stalker, and Shriek (introduced in Batman Beyond "Black Out", "Bloodsport", and "Shriek", respectively) and a new Parasite (because as shown in the Justice League Unlimited episode, "Alive!", Parasite (on Grodd's side) was killed in the aftermath of a mutiny against Lex Luthor by the Legion of Doom).
- Ace previously appeared in the Justice League episode "Wild Cards". Her appearance in this episode has a couple of redesigned details: her boots are now gray instead of black, and her club-shaped hairpin is now on the left side of her head as opposed to the right.
- The movie Terry and his family exit is titled The Grey Ghost Strikes, a nod to Bruce's childhood hero.
- Amanda's assassin is Andrea Beaumont, the Phantasm, last seen in the film Batman: Mask of the Phantasm.
- Terry reminds Waller that, despite her scrapping "Project Batman Beyond", Warren McGinnis was still murdered; the tragedy that took place during the Batman Beyond series premiere, "Rebirth".
- Bruce tells Terry to meet Kent in the Metro Tower. Apparently Terry hasn't become an official JLU member since "The Call", but only a part-timer, much like Bruce.
Home video releases
- This episode used story elements from a Batman Beyond movie that would have had Selina Kyle/Catwoman as the person responsible for the cloning of Bruce Wayne instead of Amanda Waller. Due to the dark tones of Batman Beyond: Return of the Joker, however, the second movie was rejected. The creative team decided to tie it in with the Cadmus arc. 
- There was a cut scene that explained that Waller had conducted more experiments in the past, but only stopped after Phantasm refused to kill Terry's parents.
- When Ace says to Batman, "I'm dying very soon, aren't I?", Batman responds, "Yes. I'm sorry".. However his lip movements read the words "You are" in place of "yes".
- Though it may be coincidence, it's interesting to note that in Bruce's dog is named Ace. One could say that he named the dog after Ace from the Royal Flush Gang.
- When Waller first confronts Terry in her home, Terry is standing by the desk and Waller is standing in the doorway. After the opening credits, they have switched places.
- In the B&W fighting scene, after Shriek falls down and his helmet is shattered, he can be seen not wearing the headphones he used in "Babel" and "Where's Terry?" to overcome his deafness. Either he has recovered his hearing (or was using the helmet to hear) or this is an oversight on behalf of the animators.
- When Terry confronts Bruce in the Batcave, the original Batsuit in the display is replaced with Terry's, despite Terry still wearing it.
- The final scene features Terry flying silhouetted against buildings and startling an airborne police craft, in a reversed version of the opening scene with the original Man-Bat in "On Leather Wings", the very first episode of Batman: The Animated Series and the DCAU. Likewise, "Did you see that?" is mirrored as the last line of this episode (both lines are spoken by Kevin Conroy, voicing one of the officers on board the police craft). 
- This episode marks the first time that the Batman: The Animated Series theme has been officially adapted for Terry instead of Bruce. In Batman Beyond, it was only used in the episodes "Disappearing Inque" and "Out of the Past" when Bruce himself was back in action.
- Terry's outfit and hairstyle mirrors Bruce's out of costume appearance in Justice League, "Starcrossed".
- The episode was written and produced before Justice League Unlimited was renewed for an additional season, so the episode was also intended as an epilogue for the entire DC Animated Universe started in Batman: The Animated Series, all the way to Justice League Unlimited. 
- Although it is ambiguous on-screen, producer/writer Dwayne McDuffie confirmed that the black-and-white sequences are Terry's imagination of what will happen if he resigns as Batman, not flashbacks. There are several clues that support this:
- In the black and white sequence, Terry smashes the clock down. By the end of the episode, the clock is intact.
- In the black and white sequence, Bruce was uncharacteristically forthcoming in his exchange with Terry. Also, in the final scene, he speaks casually with Terry. If such stern spat had taken place, it would be unlikely of him to dismiss it.
- Terry breaks up with Dana in a black and white scene, but later on, he calls her over the phone and she reacts too casually for someone who had just been dumped.
- According to Bruce Timm, Wayne is also the biological father of Terry's younger brother Matt. 
- According to writer Dwayne McDuffie, Bruce, as the world's greatest detective, was aware that Terry and Matt are his genetic offspring some point after Terry assumed the role of Batman and realized the machination of Amanda Waller and Project Cadmus, but would never bring it up as he wanted Terry to be his own man, and out of respect for Warren McGinnis as well since he was the one who raised him since birth. 
- Bruce Timm stated that at this point, Bruce has effectively retired from crime-fighting.
- Ace's Fantasy, including the Queen, resembles many of the illustrations and movie adaptations from Lewis Carroll's Alice's Adventures in Wonderland.
- The new Royal Flush Gang bear specific in-joking in each of their identities:
- Ten has a white swimsuit and blond cornrows just like Bo Derek in the movie 10.
- Jack is a samurai, thus putting a spin on the Cartoon Network character Samurai Jack. When this character is returned to normal, he bears a resemblance to Phil LaMarr, who voices Samurai Jack.
- Queen is revealed to be a man, thus a "drag queen".
- King looks like MODOK, a Marvel Comics character created by Jack "The King" Kirby.
- Waller's quip about the this Royal Flush Gang being the second or third incarnation of the group alludes to the fact that production-wise this is the third one. It also points out that the existence of its first incarnation from "Wild Cards" contradicts the existence of the group established in the Batman Beyond episode "Dead Man's Hand", reportedly to be century-old.
- In the shots of the suits in the Batcave, the Bruce's Batsuit from The New Batman Adventures has been replaced by Terry's.
- Throughout Batman Beyond, Terry refers to Bruce as "old man", which is a general term used for one's father. Before entering the cave to suit up, Bruce comments that Terry's "a stubborn piece of work" to which Terry quietly replies "Just like my old man".
- "Project Batman Beyond" marks the first and only time the term Batman Beyond is used in-universe.
- Kai-Ro's new uniform resembles the costume John Stewart and Katma Tui took when, after the Crisis on Infinite Earths, Green Lanterns began customizing their costumes.
|Will Friedle||Batman/Terry McGinnis|
|Kevin Conroy|| Batman/Bruce Wayne|
Sky Patrol Officer (uncredited)
|CCH Pounder||Amanda Waller|
|Lauren Tom|| Dana Tan|
Doctor Light (uncredited)
|Marc Worden|| Parasite II|
Terry: How could you do it to me, Bruce?
Amanda Waller: It's been many a year since I had a handsome gentleman caller. Why is it that superheroes are always... so good-looking?
Terry McGinnis: You know why I can't marry you. If-
Amanda Waller: Bruce's DNA was easy enough to obtain. He left it all over town. (Terry raises eyebrow) Not remotely what I meant.
Amanda Waller: You're not Bruce's clone, you're his son. There are similarities, mind you, but more than a few differences too. You don't quite have his magnificent brain, for instance. You do have his heart, though, and for all that gruff exterior, I've never met anyone who cared as deeply for his fellow man as Bruce Wayne, except maybe you.
Bruce Wayne: You're a stubborn piece of work—you know that?
(Batman flies past a police hovercar)
- ↑ In Batman Beyond, "Rebirth, Part I"
- ↑ Idem, "Rebirth, Part II"
“ Especially once you realize the 'flashbacks' never, in fact, happen, it's clear that Bruce has willingly 'retired' completely from Batman, confident that Terry will carry on his tradition, and his beloved Gotham will always be protected. Note that he says Superman called, wanting Terry's opinion on a case, not Bruce's. The idea being that Bruce doesn't actively participate in crime-fighting anymore, not even in an advisory capacity—he probably doesn't even monitor Terry on the com-link anymore [...]. The 'soup' bit implies that he's taken on the 'Alfred' role, and though he nags Terry about the soup going cold, he seems pretty confident with his lot overall. ”
— Bruce Timm,