Ten years in the future, Amity Park is a bustling future metropolis protected by a large ghost shield, operated and run by Damon Gray while his 24-year-old daughter, Valerie Gray serves as the city's sole protector from ghosts, particularly one who uses his newest power, the Ghostly Wail, to easily break the ghost shield and conquer the world. Valerie flies away on her hoverboard, only to be further ambushed by the Fright Knight who's now in servitude to the ghost that broke the shield. She heads to safety in the Fenton house, now occupied by her and her father. Unfortunately, the powerful ghost gets through from below and blows up the entire house. All this is being watched by Clockwork, ghost master of time as the mysterious Observants explain to him that the powerful ghost is Danny Phantom ten years into the future. Clockwork's job is to destroy the current Danny Phantom to ensure he never grows up to be the world's most evil ghost.
Back in present time, Lancer makes a public announcement to everyone in school about the CAT which will help determine their future, one test Danny takes seriously. Jazz already passed with flying colors while another classmate named Irving failed, later defending his job in the Nasty Burger, saying if the boiler is messed with in the wrong way, the entire place would blow, something none of the students care for. Lancer then locks the test answers in his briefcase, going as far as handcuffing himself to it. Clockwork watches all this from his headquarters while the Observants push him to destroy Danny (since the two only observe and never act). Clockwork obliges.
Back home, Jazz tries hard to help Danny succeed, but he's more frustrated that she's smarter then he ever will be and how little success he feels he will gain. He is then hit by the Boo-merang, a Fenton boomerang device designed to home into a ghost's unique ectosignature, something which it keeps doing with Danny. His parents grow confused on why it keeps targeting Danny, then take off with it.
Clockwork comes and freezes time, then sends Box Lunch (daughter of the Box Ghost and the Lunch Lady Ghost) after giving her a time medallion to ensure her stay in another time period from the future to destroy Danny. Jazz quickly leaves upon seeing the ghost to let Danny handle the battle and the two fight, eventually flying all the way to the Nasty Burger where his friends and Mr. Lancer are. Battling inside, Danny remembers Irving's words and sends a condiment towards Box Lunch, causing the Nasty Burger to blow up halfway (and the boiler room inside slowly to rise in heat), sending Danny back where he goes straight through Lancer's briefcase (upon turning intangible for safety). Once everyone runs away in panic, Danny finds the time medallion Box Lunch had (who has since been sent to her own time period upon losing it) as well as the answers to the CAT test. As a result, with the Observants pushing him, Clockwork sends another ghost to fight, even though his future is sealed or so he claims.
The next day in school, Tucker and Sam berate Danny for his possible plans to cheat on the CAT, something Lancer overhears. Opening his suitcase to find his test answers gone, he calls for Jazz to talk with him after school where he reveals to her that Danny stole the answers. Jazz tries to defend him, stating he has no proof, so Lancer gives Danny until the day of the test to return it.
Back in the Fenton household, Tucker tries to figure out the time medallion, but gets no results. Danny then gets ready to look at the answers to the test (much to his friend's dismay) until he meets another ghost from the future: the combined forces of Skulker and Technus, the SkulkTech 9.9. A long battle between the two ends when Danny's powers are shorted out by SkulkTech and then captured by a mechanical claw by the two. Tucker hacks a way into their system, causing them to fall onto a lamp post, their time medallion slipping off as well, sending Skulktech as well as Danny, Sam, and Tucker (when the latter two tried to pry the claw off of him) to Clockwork's lair.
Inside, the trio finds the only portal to the future, witnessing the destruction Danny's future self is causing over there. Clockwork then appears with seeming intentions to kill Danny and prevent his dark future. Danny tries fighting Clockwork but with his advantage of controlling time on his side, it's a one-sided battle he nearly wins. Luckily, Tucker has managed to figure out how the time medallion works, protecting them from all sorts of time-based altercation. After he gives one each to Sam and Danny, Clockwork decides they have seen too much and summons other iterations of himself to prevent them from altering the timeline. With nowhere else to go, the trio escape through the future portal to get away from Clockwork.The future already proves grim for the three and even more so when future Valerie catches (young) Danny, ready to exterminate him. Sam and Tucker step in to stop her, only for her to be shocked at the prospect that they are alive. Dark Danny then appears and sends Valerie away, rescued only by Danny, but then she passes out. In the meantime, Sam and Tucker run away, only for Dark Danny to drop the rubble of the Fenton household on them through his Ghostly Wail. Luckily, they took off their time medallions, safely returning them to their own time period. Unfortunately, Dark Danny places Danny's time medallion inside of him, unreachable by either ghosts or humans, and throws his past self into the Ghost Zone.
Sam and Tucker end up in an alley near the Nasty Burger where Jazz confronts them, having discovered Danny indeed had the test answers. She warns them both that Danny better fess up or else. Afterwards, Sam theorizes Danny cheating is what will lead him to become his evil self. Back in the future, Danny finds out his family, friends, and Mr. Lancer were all killed when the boiler exploded with them inside. Dark Danny afterwards comes to him, telling his past self that he plans to ensure his future still exists, so after he sends his past self to the Ghost Zone to keep him from causing any further distraction, he uses one of the time medallions to travel back into the past.In the present time period, Dark Danny (disguised as his 14-year-old past self) reunites with his former friends, telling them both he has beaten his evil self and that the Nasty Burger boiler is also taken care of (when in reality, it's still ready to blow). Back in the future Ghost Zone, Danny meets up with all the ghosts he has defeated previously, all the worse after having encountered Dark Danny (Johnny 13 is in a wheelchair and pushed around by his shadow, Ember McLain is overweight and has severely damaged vocal chords, etc.). As an act of revenge, they gang up on him.
Back in the present, Dark Danny returns to his room (where the Boo-merang is also located) and meets Jazz who confronts him on his cheating, later confessing she knows he is half-ghost, and proud of what he does, until now. A bit shocked she knew, Dark Danny turns into his normal form, prompting Jazz to finally figure out he isn't Danny, seeing as how even the Boo-merang wouldn't home in on his ecto-signature. Dark Danny confirms that he is her brother and that his past self is floating in the Ghost Zone in the future. Jazz defiantly claims that her brother will beat him, Dark Danny highly doubts it. He's destroyed the Fenton portal in the future but he has yet to find the one belonging to his "cheese head of an arch-enemy" (which Jazz guesses to be Vlad Masters) and stuns her unconscious.Jazz wakes up the next day to find Dark Danny had already left to take the test. Quickly, Jazz takes the Boo-merang and ties on a note she hastily wrote with her headband, sending it to the Ghost Zone in hopes it'll reach Danny in 10 years. Back in the future, frustrated with the massive wave of ghost attacks, Danny suddenly gains the ability to use the Ghostly Wail, knocking them all unconscious. Afterwards, the Boo-merang finds him. Danny reads the note, seeing Vlad is involved and goes to track him down. Meanwhile, Dark Danny starts to cheat on his test, something his friends still are livid over. Jazz watches from afar, ready to destroy him with the Fenton Ghost Peeler, only for Dark Danny to notice, sending an invisible duplicate of himself to knock her unconscious and drag her away.
Danny manages to find the portal to Vlad's manor, but upon entering, the manor has since been long gone and the once proud billionaire is now a depressed old hermit. Seeing Danny and guessing that he's from the past, he relates the story of how Dark Danny was born: after the death of his loved ones, Danny moved in with Vlad, seeing as he was the only other who could understand his pain. Wanting to make the hurt go away, he requested to Vlad to remove his ghost half, something Vlad honored, pulling it out with Ghost Gauntlets. However, once freed from his human self, Ghost Danny went berserk, took the gloves and ripped Vlad and his ghost half apart. He then possessed Vlad's ghost, his evil side ultimately taking control of him and turning him into the evil incarnation he is now. Blowing up Vlad's manor, and supposedly killing his human half, Dark Danny left to begin his ten year rampage of world destruction. With the story over, Vlad laments that he spent the ten long years stuck in regret and guilt for all the damage he had caused. Danny, in a rare moment, forgives him, then asks for his help to take out the medallion inside of him using the Ghost Gauntlets. Readying his gadgets, Vlad remarks that perhaps he could eliminate Danny before he becomes evil and strikes.
Dark Danny has finished his test and walks off, prompting Lancer to call his parents and arranges a meeting at the Nasty Burger. There he reveals Danny cheated which shocks the parents. Sam and Tucker then come over to warn them the boiler is about to explode while Jazz, complete in Fenton Ghost Peeler gear reveals Dark Danny's true form to the others. Already his parents are on the offensive, demanding to know where their son is, only for Dark Danny to reveal himself as their child. He smugly taunts the fact that his parents, the world's two leading ghost experts, couldn't figure out that their own son is half-ghost (Jack tells Maddy that for the record, he blames her).
Dark Danny even points out that there was a rhyme between Fenton and Phantom and that Jazz was the only one to figure it out, much to Tucker and Sam's surprise. He then ties up his family, friends, and Mr. Lancer to the boiler where the explosion would kill them. Danny then comes from the future with a gear of Fenton gadgets, ready to duke it out with his darker future self.
A battle rages, Dark Danny ensures the battle drags out long enough for Danny's friends and family to die, believing that the fact he still exists is proof that he shall be Danny's future. However, he grossly underestimates his past self, as proved when Danny suddenly uses the Ghostly Wail on him. Shocked he gained a power he would not receive for another ten years, Dark Danny is struck by another Ghostly Wail, causing him to crash into a building. Danny then sucks him up with the Fenton Thermos. Unfortunately, with the last wail taking a lot of his energy, Danny cannot transform back into his ghost half, making him too late to stop the explosion.
Time freezes however and Danny finds him next to Clockwork who had saved his loved ones, now knowing that the time master knew everything that was to happen. He explains to Danny that the Observants view time as a parade, watching each event happening in sequence, whereas he sees the parade from above, where all the twists and turns may or may not happen. Giving him a second chance, Clockwork sends Danny back into the past before the start of the test where Danny confesses he was going to cheat, much to the relief of his friends and sister. Given another chance to take the test, he goes out to the front of the school where he gets Jazz to confess that she knows his secret. With that said, the two embrace, Jazz now part of Danny's team. He then goes off to fight off a giant ghost nearby. As they do battle, Jazz is splatted with ectoplasm, and comments that this is going to get some getting use to.
Back in Clockwork's home, the Observants cry out to Clockwork, stating he cheated to get Danny to influence his choice. Clockwork answers, stating Danny made up his own mind despite his little cheat. The Observants then make a note that he is to be the sole guardian of Dark Danny now that he exists outside of time. Clockwork merely agrees, knowing everything that has happened and will happen, then he places the thermos away, where Dark Danny struggles in vain to escape...
- The "pole thing" (where Danny and then SkulkTech are falling to only catch a pole to break their fall) is a reference to the Spider-Man comic series. Both times, the protagonist loses his powers before catching onto the pole.
- Jazz's car seems to resemble a Volkswagen Thing.
- When Valerie blasts Dark Danny into the street, he sticks his hand through the dust and then clears it, this is homage to One Piece when Luffy knocks back CP9 member Blueno into the side of a building and he does the same motion.
- The movie has some similarities to Marvel Comics' Incredible Hulk: Future Imperfect, where the Hulk is taken to a possible future to fight his evil older self, the Maestro.
- Dark Danny is similar to the X-Men villain Onslaught, who came to existence from Professor X's dark side combined with Magneto's consciousness. He also bears some resemblance to the Spider-Man villain Venom, which is particularly stressed when he extends his tongue.
- Clockwork's ending speech is from Neil Gaiman's Sandman character, Delirium.
- Dark Danny also slightly resembles the superhero Freakazoid, from the 1995 cartoon of the same name. Interestingly enough, David Kaufman, the voice of Danny, did the voice of Freakazoid's secret identity, Dexter Douglas.
- Many fans of this show consider The Ultimate Enemy to be the darkest episode in this entire series, some even as go as far to compare this episode to Batman: The Animated Series episodes.
- Introduced Ghost Powers: Ghostly Wail
- This is the third time in the series where Danny's ghostly and human halves are separated. The first two are in "What You Want" (which was purely accidental) and "Identity Crisis" (where Danny did the separation himself).
- This also marks the second time Danny turns to the dark side (the first time being Control Freaks).
- This episode is tied with "Maternal Instincts" as Butch Hartman's favorite Danny Phantom episode.
- This is the second Butch Hartman TV movie in which the protagonist meets his older self from an alternate future. The first was "Channel Chasers", a Fairly OddParents 90-minute-long TV movie. Timmy's older self was masked for most of his screentime, and his constant pursuit of his younger self led young Timmy to believe the figure was a villain. The respective older selves also time-travel in the respective episodes.
- There is a major time travel logic flaw. Danny turning evil is dependent on his friends and family being killed in the explosion, yet he (his future self) causes them to be killed. It would be illogical for someone's evil form to cause the event that caused them to turn evil, although this could be seen as an example of predestination paradox. Further, because Danny had discovered the full story of Dark Danny's origins from talking to Vlad in the future, it is likely he would know not to go to Wisconsin and undergo the procedure of having his ghost half removed (Although it is possible Danny was to hurt to care and wanted to do anything he could to heel the pain). However, since the Observants have asked Clockwork to prevent this future, it's possible that the original explosion was caused by a different event, thus Dark Danny was trying to undo Clockwork's attempts to prevent it
- The future Vlad never explained how the Nasty Burger exploded, but it's shown that Clockwork sending Box Lunch then Skulltech to fight Danny are what causes it in the episode. The explosion from the fight with Box Lunch puts the heat lamp close enough to warm up the vat of Nasty Sauce, then the battle with Skulltech pushes it even closer, speeding up the process.
- It is revealed that the phone number of the Fenton Works is 555-1221.
- First and only appearance of Dark Danny. First appearances of Clockwork and the Observsants.
- The "Observants" had a similar job and problem as "The Watchers" from Marvel Comics, having sworn only to watch events and never intervene or effect them. The Observants are mentioned to never act, only watch though they indirectly changed the timeline, asking Clockwork to destroy Danny Phantom as a kid. Though this meant that THEY never did anything directly they did influence time by asking Clockwork to kill Danny and therefore did change the timeline.
- Dark Danny is Danny's unlockable costume in "Nicktoons: Attack Of The Toyboys" but the costume being named "Evil Danny".
- The last episodes of Ben 10: Ultimate Alien, divided in Part 1 and Part 2, has the same name of this special.
- This is the first and last time Jack calls Danny "Dan". (While he's studying for the CATs)
- This episode reveals that ghosts age and can have children (Boxlunch)
- The episode is similar to the episode of Doctor Who "The Ultimate Foe" where the Valeyard , an evil future regeneration of the Doctor, wanted to kill him to free himself from its influence.
- When Valerie gets hit by the Fright Knight, she does not have any bruises. But later when she falls to the ground, she is seen with them. It may be that she didn't get the bruises from the blast but from the landing.
- In the first shot of Dark Danny cheating on the Career Aptitude Test, it is misspelled as "Careear Aptitude Test".
- When Clockwork shows what's about to happen to the observants, right after he gives the answers to Danny, we can see a scene where Danny fights Dark Danny, whose beard is black and not white.
- Clockwork's medallions disappear and reappear throughout various scenes and from characters when they're supposed to be constantly worn (Such as Skulktech 9.9 not seen wearing one until it falls off). Surprisingly, Danny did not return to his time whenever Dark Danny removed his medallion to fuse him with it (though it may have been because Dark Danny was in contact with both him and the medallion, as the temporal effects seem to extend to people in physical contact, otherwise, Skulktech could not have brought them with him when he went back to Clockwork's lair).
- When Danny is fighting Dark Danny for the 2nd time, he puts the Spector Deflector on him, but amazingly the gloves stay on the belt when he lets go.
- When Dark Danny fuses Clockwork's time medallions into Danny, it remains in his hand after he puts it inside Danny when it shouldn't.
- A close-up on Danny's face when he says, "Time's up!" shows him in his ghost form (with white hair and green eyes), even though he was forced out of it (by using his ghostly wail) a moment before. In the shot immediately afterwards, (when he uses the Fenton Thermos on Dark Danny) he is in his human form.
- At the beginning, Dark Danny destroys FentonWorks completely, but later on when Danny, Sam, and Tucker end up in the future, right before Sam and Tucker go back in time, the building is still there, Considering the Ops-center still retains the crack in the middle as it did earlier, it could've merely been re-built.
- When Vlad is telling Danny about the death and how he came to him. When Danny looks at the picture of his family and freinds it is taken in front of Fenton works but in the picture it just say Fenton.
- In this episode, the Ghost Gloves from episode 5 are changed to the Ghost Gauntlets. It's not shown how Vlad managed to get them.
- When Danny's family and friends are first shown to be killed by the explosion:
- Maddie has her hood on, yet later on when the same event occurs at the end of the episode, her hood is down.
- Danny says "No!" after the explosion, but when the real events occur near the end of the show, he says it before the explosion, though it could most likely be because he knew it would happen.
- The form of the explosion is similar to the form of an atomic bomb explosion, but once Dark Danny is captured, the form is more of an outward explosion.
- When Danny and Clockwork go back in time to CAT testing by the end by two hours early, the clock shows that it's five to nine despite Lancer asking to meet the Fentons at 5PM.
- When Clockwork says, "You must be eliminated before you permanently alter the timestream." he is in his old form. Immediatly afterwards (when he makes other versions of himself appear), he is in his adult form. Right after that, he is in his old form again.
- When Clockwork takes Box Lunch to the past, his scar on his face switches from his left side to his right.
- When Vlad tells Danny about what happened to his friends and family the front page of the newspaper has a picture of the Nasty Burger totally wiped out by the explosion, although in the future scenes and immediately after the explosion at the end of the episode parts of the building remain.
- Dark Danny duplicates himself into four copies to fight Danny. But after he overpowers the present Danny, Dark Danny is seen with five copies instead of four.
- When Danny, Sam and Tucker first go to the future and Valerie traps Danny in a ghost net, you don't see his colors. But when they first meet Dark Danny (after the commercial break) you can see the colors through the net (which were not visible before).
- Dark Danny's ponytail is flamming in some parts of the episode along with the rest of his hair and sometimes, it's completely motionless.
- After Danny uses his ghostly wail for the first time when he changes back only his head changes. (Though this might be because of the time medallion or because it was his first time using it, so it wasn't as powerful and didn't drain him as much, so he only partially reverted back.)
- Just before Danny catches the flag pole, he is seen with green eyes while he is in his human form.
- When Danny uses his ghostly wail, only his hair changes back to human.
- At the end of the episode when the Observants are reprimanding Clockwork, the Fenton Thermos containing Dark Danny is missing the lid.
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