The story is set roughly 8-9 years after "What About Mimi" with Grim Jr., Minniemandy and Mimi are now young adults and Mandy has given birth to the twin son and daughter of Dan Phantom Daniela Phantom and Manny Phantom.
Grim Jr. is sleeping on a rock somewhere in the Underworld when he is awoken by a rather nasty dream involving his sister whom declares that she should have left him to die. Junior has another argument with his Nergaling about the recent string of child kidnappings in the underworld. While the Nergal wants to investigate the disappearance of Mina Harper for Vlad the Count Junior is not interested in work without pay.
The next day Junior returned to Castle Evergrim for the first time in 3 years for Minnie's 20th birthday. He interrupts his twin siblings Manny and Dani in yet another of their infamous fights, which Daniela seem to be winning despite the fact that she's not really fighting back. During the fight Manny lands a hit that sends his sister flying into their older brother.
Dani initially reacts with disgust to Junior and in particular his Nergaling, the latter commenting that Dani literally looks good enough to eat. "Jokes" aside Junior questions why the twins are trying to kill each other, according to Dani they were having another argument about how they treat each other. The fight is ultimately broken up their mother Mandy whom instructs the pair to return to their studies.
The twins guess that Junior is back for Minnie's birthday, to which they inform the celebrations were canceled. Junior goes through the castle looking for Minnie and ultimately stops at her room. There he reminisces about their tear jerking separation three years ago: Junior was beginning to lose control of his powers and chose to leave in order to protect his family, especially Minnie who was heartbroken to lose him.
Furthermore Junior has felt nothing but guilt for leaving Minnie behind, even after having gained complete control over his vast power he stayed away for years longer then he had to so that he could go on adventures around the Underworld and someday come home, feeling as if the time he spent away could be justified only to finally work up the courage to come home and discover his sister not even home.
Meanwhile Grim and Mandy are discussing Minnie and Junior. Grim does not wish to break Junior's heart by telling him the truth about Minnie's disappearance but Mandy points out that he's grown up from the child that would have bent to their every whim and he'll be furious with them when he finds out. Sadly Junior overhears the conversation and threatens his parents with his powers demanding to know where Minnie is.
Mandy explains that they initially believed Minnie had left on her own volition three months ago on her own journey working under the belief that Junior abandoned her because of her ageless body. However they've recently received a letter from their "old friend" Boogeyman stating that he has Minnie and will only return her in exchange for Grim's scythe.
Junior is understandably enraged to learn that his parents have done nothing to save Minnie and flies off through a newly blown hole in the wall in search of her. The twins spied on the whole exchange and ultimately decide to aid their brother in looking for her. Dani instructs Manny to hold her hand, Manny entirely misinterprets Dani's intentions leading to Dani to forcibly render them both invisible and chase after Junior.
Meanwhile Minnie, now missing both of her eyes, is walking through Boogeyman's Castle when the latter catches up with her. He sweet talk's the depressed Minnie and informs her that some individuals were spotted leaving Evergrim, apparently in search of her, and that Junior is causing a ruckus in the underworld asking for them.
Boogieman has his servant Empheles go spy on, and if necessary kill, Junior to learn any valuable information about the Grim Reaper while he prepares for his and Minnie's wedding. Drax, Boogieman's resident mad scientist, goes to make some adjustments to Empheles before he leaves so that he may watch the proceedings on his computer.
On his way out Drax expresses his interest in Minnie and confesses that if she weren't already his master's he'd take her for his own experiments, leading to Minnie to smack him for his vulgar and disrespectful speech. Meanwhile Junior finishes killing another monster and camps for the night. The twins are still spying on him and Manny complains that he's hungry and wondering why they're spying on Junior.
Empheles, meanwhile is watching the trio, Drax wants to know how Empheles stands up against the famed Grim Reaper. Empheles however, points out that this is suppose to be a reconnaissance mission. Before Drax can emphasize his point about that he is Empheles one true master he notes that there's something unusual about the twins and orders his computer to study them further.
Junior makes contact with Mimi and asks her if she can find some information on Boogieman's messenger Empheles. Manny catches sight of Mimi and follows his perverted instincts to move closer to get a better look at her despite Dani warning him that he'll catch them. Drax meanwhile concludes that the twins are ghosts, powerful ghosts no less, and orders their immediate capture.
Manny meanwhile has managed to give himself away when Mimi noticed him, furthermore neither of the brothers are able to act in time when Empheles manages to take Dani hostage and teleports her back to Boogieman's castle. Later Manny is crying over not being able to save Dani. Junior gives Manny a soul to eat while Mimi does some research for them.
According to Mimi Empheles is a Basilican, a species of powerful Demon that was created in the image of, and subsequently wiped out, by Lucifer himself. Junior notes that a Basilican was suppose to be responsible for the recent kidnapping of children across the Underworld, and finally it's highly unusual appearance, like it was a cyborg of some kind.
To this end Mimi uses Googhoul to search for Basilican sightings and gets one hit. Meanwhile Dani awaken's hooked up to some machinery and demands an explanation. Drax starts by explaining that his associate Empheles is a Basillican he revived as a cyborg and that the machine is designed to drain Dani of her powers and energies which will unfortunately kill her as a result.
Drax also instructs Dani to discard her faith in her brothers claiming that family is simply a hindrance, he should know as he killed his own sister when she got in his way. Reminiscence aside Drax begins the procedure rendering Dani unconscious when the life starts being sucked out of her. Manny feels Dani's pain and luckily both he and Junior are already on their way.
Deciding to pick up the pace Manny bolts off to the castle without his brother and gets captured by Drax's containment field, leading Junior to note that he's rescuing all of his siblings tonight. Meanwhile Drax brings Manny inside his lab and begins his physical and psychological assessment, showing a measure of disappointment since he expected more from Mandy's last son and based on what he heard from Dani.
When Manny asks what happened to Dani Drax explains that her life force is being drained and added to his Harvester machine, a fate that Manny will share. Enraged with the mad scientist Manny uses his Ghostly Wail to break free of the containment bubble leading Drax to conclude that he doesn't need both twins and orders Empheles to kill the young Halfa.
Junior meanwhile tears apart Boogieman's forces and breaks into the castle. Boogieman explains that he won't be getting back any of his siblings tonight: the twins will likely not survive Drax's sick experiments and Minnie has no intention of returning home letting her confirm it herself. Minnie refuses to speak with Junior and reveals that she is missing both of her eyes.
Boogieman reveals that when Minnie learned that he was planning on handing her over to her parents for Grim's scythe she gave him her other eye, and as per the tradition of the Nergals she is set to be married to him. Meanwhile Empheles is about to kill Manny off, in spite of Dani's attempts to convince Manny to use his full range of powers.
Manny finally listens to his sister as the blade is about to pierce him and as a result Empheles destroys Dani's restraints instead. Meanwhile Junior and Boogieman are arguing, Boogie explaining that he has been watching their family since long before Junior was born and that they both now have part of Minnie inside of them. Seeing Minnie's dark future through her eye Boogieman doesn't blame Junior for abandoning her.
Sufficiently enraged now Junior attempts to attack Boogieman but Minnie orders him to stop. Junior decides to prove his sincerity that the power Minnie has given him means nothing to him without her by giving her back the eye she gave him so long ago, Junior collapsing with the eye no longer sustaining him, he realizes that the reason he's felt empty for so long is because he hasn't had Minnie in his life.
Meanwhile Manny and Dani have taken advantage of Drax taking five minuets to inform Empheles that "he is Stoopid" to bring out their new trump card: Dani has used her self-replicating powers to create 7 clones of herself and Manny while all the Manny's blast the pair with his Ghostly Wail. Meanwhile Boogieman accepts Junior's offer for his powers in exchange for his siblings and orders Creeper to retrieve the twins.
However Boogieman reveals that he is keeping his fiance Minnie, whom has already made it clear she has no intention of leaving with Junior and states that he should have stated his terms before removing the eye. Boogieman explains that he intends to add the eye to his collection of life force collected from only the most powerful species of Monster in the underworld, or more specifically their children.
Junior realizes that Boogieman is responsible for the missing children and has been using them in a mad quest for power. Boogieman simply explains that his only power is to scare children so he's using that to his advantage and further explains that he is only doing the job that Junior and his father are suppose to be doing which Junior can't even do now that he's given up his power.
At this Minnie wrestles the eye out of Boogieman's hand and takes it back, along with her other eye in Boogieman's head. Meanwhile the twins have succeeded in defeating Empheles the latter declaring that the twins father must be proud of them and trained them well. However the twins claim they have no father and that they taught themselves how to use their powers.
Drax decides to kill all of them with a self destruction device he planted inside of Empheles to which end the cyborg demon shows the twins the way to safety before he explodes and kills Drax. Meanwhile Boogieman decides to teach Minnie a lesson and absorbs all the powers inside of the harvester to transform himself into a huge patchwork monster to kill the entire Grim Family.
Meanwhile Creeper and his goons catch up to the twins, and seeing as how they don't appear to be ghosts they decide to get some entertainment out of beating them up. Suddenly however they are all killed when a giant wrecking ball is thrown through the wall by Mimi. Meanwhile Boogieman has pinned Minnie down and is in the process of ripping her apart, Junior however able to use a discarded Nergal wing to reap Boogieman.
At the same time Mimi, carrying the twins with mixed results, opens a hell-portal and drags Boogieman off to his well deserved fate. Boogieman's corpse releases the souls of his victims who question Junior on who he is. Minnie makes Junior a new Nergal scythe to which the children correctly guess that he's the Grim Reaper. Junior agree's with the assessment and together with Mimi takes all the children home.
In a final scene Dan Phantom arrives at the lab and ends the story when he steps on what's left of Drax's glasses.