Ten years in the future, much of the Earth has been ravaged and left in ruins. Amity Park remains as a heavily fortified city and has become a bustling futuristic metropolis. It is protected by a huge ghost shield, operated and run by Damon Gray, while his 24-year-old daughter Valerie serves as the city's sole protector from the ghosts that try to attack from outside. The ghost shield was nigh-impenetrable and had protected Amity Park for ten years, until one new, very evil and very powerful ghost uses his newest power, the Ghostly Wail, to easily break through the ghost shield. Valerie is then ambushed by the Fright Knight, who reveals he is now in servitude to the new ghost. She heads to safety in Fenton Works, now occupied by her and her father; the Fenton family is nowhere to be seen. The new ghost gets through from below, and reveals himself to be an adult Danny Phantom. He then blows up the entire house. All this is being watched by Clockwork, ghost master of time, and the mysterious Observants. As the Observants can only watch and never interfere, they task Clockwork with saving the future - by destroying the present Danny Fenton.
In the present, Lancer makes a public announcement to the students of Casper High School about the Career Aptitude Test, which will determine their future. Jazz already passed with flying colors, while another classmate named Irving failed and now works for minimum wage at the Nasty Burger. Irving tries to explain that his job is very important, because if the Nasty Burger special sauce were to overheat it could cause a massive explosion, but none of the other students seem to care. Lancer shows the students that he has the folder containing the answers to the test, then locks the folder in his briefcase. Clockwork and the Observants watch all this from Clockwork's lair. The Observants urge him to destroy, and Clockwork obliges.
Back home, Jazz tries hard to get Danny to study for the C.A.T., but this makes him even more frustrated about how he feels she's smarter than he ever will be and how little success he feels he will gain. He is then hit by the Booo-merang, a new Fenton device designed to home into a ghost's unique ecto-signature. His parents are confused why it keeps targeting Danny, and suggest that it might be malfunctioning.
Box Lunch, daughter of the Box Ghost and the Lunch Lady Ghost, comes from the future to the room Danny and Jazz are in, sent by Clockwork destroy Danny. Jazz quickly leaves upon seeing the ghost to let Danny handle the situation. Danny transforms and the two fight, eventually flying all the way to the Nasty Burger where his friends and Mr. Lancer are. Danny remembers what Irving said about the Nasty Sauce and throws a packet of it at Box Lunch and heats it with his ghost ray, causing a huge explosion that destroys half the building (and damages the machines in the boiler room, causing it to slowly rise in heat). The explosion flings Danny back to where a crowd has gathered. His trajectory takes him straight through Lancer's briefcase, which he phases through. Everyone runs away, and there is no sign of Box Lunch. Danny finds a medallion that he remembers Box Lunch was wearing, as well as the answers to the C.A.T. which he had inadvertently phased out of Lancer's briefcase. The Observants urge Clockwork to send another ghost to stop Danny, but Clockwork now ominously claims that Danny's future is sealed.
The next day in school, Tucker and Sam berate Danny for what they see as him planning to cheat on the C.A.T., which 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 has the answers and must have stolen them. Jazz tries to defend Danny, stating that Lancer has no proof, so Lancer gives Danny until the day of the test to return the answers.
Back in the Fenton household, Tucker tries to figure out the time medallion's functions, but gets no results. Danny is about to look at the test answers (much to his friends' disapproval) when he meets another ghost from the future: Skulktech 9.9, a ghost made from the combined forces of Skulker and Technus. A long battle between them ensues, which ends when Tucker hacks into Skulktech's system. As Skulktech falls, their time medallion slips off, and they, Danny, Sam, and Tucker are transported to Clockwork's lair.
Inside, the trio looks through a portal to the future, witnessing the destruction Danny's future self is causing. Tucker then finds a few time medallions and puts one on in a failed attempt to go back to the present. Clockwork then appears, seemingly wanting to kill Danny to prevent his dark future. Danny tries fighting Clockwork, but it's a one-sided battle, as Clockwork has the power of time control. Clockwork freezes Danny in place and lunges at Danny with his scythe, to try to prevent his evil future from happening once and for all. Unaffected by the time-out, Tucker figures out that the time medallion protects the wearer from all time-based alterations, and gives one to Sam and Danny, freeing Danny. Clockwork decides that they have seen too much and summons ghost soldiers from different eras to prevent them from altering the timeline. With nowhere else to go, the trio escapes through the portal to the future.
The future already proves grim for the three and even more so when future Valerie catches young Danny, ready to exterminate him, but she is shocked that Sam and Tucker are alive. Dark Danny then appears and sends Valerie away. Danny rescues her and she then passes out. In the meantime, Sam and Tucker run away, only for Dark Danny to drop the rubble of the Fenton house on them with his Ghostly Wail. Before they are hit, Sam takes off their time medallions, safely returning them to their own time period.
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, saying that she'll talk to Mr. Lancer if Danny doesn't confess. Afterwards, Sam theorizes that Danny cheating is what will lead him to become evil.
Back in the future, Danny finds out his family, friends, and Mr. Lancer were all killed when the Nasty Burger boiler exploded with them inside. Dark Danny comes to him, telling his past self that he plans to ensure his future still exists. To bind young Danny to this time, he places his past self's time medallion inside of him, unreachable by either ghosts or humans, and throws him into the Ghost Zone to keep him from causing any further distraction. Then, Dark Danny disguises himself as his 14-year-old human self and uses one of Tucker's time medallions to travel back to the present. The disguised Dark Danny reunites with his former friends in the present, telling them he has beaten his evil future self and that the Nasty Burger boiler is also taken care of (while in reality, it's still ready to blow).
In the future Ghost Zone, Danny finds the future versions of all his Ghost Zone enemies, all the worse after having encountered Dark Danny. Johnny 13 is in a wheelchair and pushed around by Shadow, Ember is overweight and has severely damaged vocal chords, and even the Box Ghost has an eye patch and a hook hand from being used as Dark Danny's punching bag. As an act of revenge, they gang up on him.
Back in the present, Dark Danny returns to his former room in the Fenton house, where Jazz is waiting to confront him on his cheating. She then confesses that she knows he is half-ghost and is secretly really proud of him for everything he's done. A bit surprised that she knew, Dark Danny turns into his normal form. Dark Danny confirms that he is her brother and that his past self is floating in the Ghost Zone in the future. Jazz defiantly says that her brother will beat him, which Dark Danny highly doubts, as he destroyed the future Fenton Works' ghost portal.
Jazz wakes up the next day to find Dark Danny has already left to take the test. Quickly, Jazz takes the Booo-merang, ties a note to it with her headband, and sends it to the Ghost Zone in the hope that it will reach Danny in 10 years.
Back in the future, Danny is helpless against the ghosts attacking him. In his frustration, he suddenly gains the ability to use the Ghostly Wail, knocking all his enemies unconscious. Soon after, the Booo-merang finds him. Danny reads the note, realizes that Vlad is involved, and goes to track him down.
Meanwhile, Dark Danny starts to cheat on the test, something his friends are still livid over. Jazz watches from afar, ready to destroy him with the Fenton Ghost Peeler. Dark Danny notices and sends an invisible duplicate of himself to knock her unconscious and drag her away.
Danny manages to find the portal to Vlad's manor (hidden behind a giant football), but upon entering, he notices that the manor is long gone and the once proud billionaire is now a depressed old hermit. Seeing Danny and guessing that he's from the past, he tells the story of how Dark Danny came to be: after the death of his loved ones, Danny moved in with Vlad, as he was the only one who could possibly understand his pain. Wanting to make the hurt go away, he requested Vlad to remove his ghost half, something Vlad honored, pulling it out with the Ghost Gauntlets. However, once Danny's ghost half was removed, it went berserk, took the gloves, and ripped Vlad's ghost half out of him. Danny's ghost half then attempted to overshadow Vlad's ghost half, only for the two ghosts to fuse and Vlad's evil nature overwhelming Danny, becoming 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. 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 he could instead eliminate Danny before he becomes evil, and strikes.
In the present, Dark Danny finishes the test and walks off, prompting Lancer to call his parents and arrange a meeting at the Nasty Burger. There, he reveals his suspicions that Danny cheated, shocking his parents badly. Sam and Tucker then come over to warn them that the boiler is about to explode. Jazz arrives as well and blasts Danny with the Fenton Peeler, revealing Dark Danny's true form to the others. Alarmed, his parents are on the offensive, demanding to know where their son is, only for Dark Danny to reveal himself as their child.
Dark Danny smugly taunts his parents, saying how they claimed to be world's leading ghost experts yet couldn't figure out that their own son is half-ghost. They never even made the connection between the names Fenton and Phantom. Jazz was the only one to figure it out, much to Tucker and Sam's surprise. Dark Danny 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 bunch of Fenton gadgets, ready to duke it out with his darker future self. A battle ensues. Dark Danny makes sure not to kill his younger self, as all he needs to do is stall for time so that Danny's friends and family die in the explosion, ensuring his future. However, he grossly underestimates his past self when Danny suddenly uses the Ghostly Wail on him. Shocked that he already gained a power he should not get for another ten years, Dark Danny is struck by another Ghostly Wail, causing him to crash into a building. Danny then captures Dark Danny in the Fenton Thermos.
Unfortunately, with the last wail using all of his energy, Danny cannot transform back into his ghost half, making it too late for him to stop the explosion, and all he can do is look on in grief and horror. Time freezes, however, and Danny finds himself next to Clockwork who has saved his loved ones. Clockwork explains to Danny that the Observants view time as a parade, watching each event in sequence, whereas he sees the parade from above, along with all the twists and turns that might or might not happen. Giving him a second chance, Clockwork sends Danny back into the past, before the start of the test, where he returns the test answer booklet and then confesses he was going to cheat, much to the relief of his friends and sister. He goes out to the front of the school, where Jazz meets him and she confesses that she knows his secret. With that said, the two embrace, Jazz now part of Danny's team. A giant ghost then attacks, and Jazz gives her brother one last hug before letting Danny go to fight the ghost. As they battle, Jazz is splatted with ectoplasm, and comments that "this is going to get some getting use to."
Back in Clockwork's lair, the Observants accuse Clockwork of cheating to influence Danny's choice. Clockwork answers that true, he cheated, but stating Danny made up his mind on his own nonetheless. The Observants then give the thermos containing Dark Danny to Clockwork, as Clockwork is to be his sole guardian now that Dark Danny exists outside of time. Clockwork merely agrees, saying that he knows everything that has happened and will happen. He then puts the thermos away. The last thing seen is the Fenton Thermos, from which Dark Danny struggles in vain to escape...