Hihi!! Im so glad u asked :) ive talked about it before on twitter but i love to yammer about it (and i much prefer textposting on tumblr) so i dont mind doing it again!!
In short, Dr Ms The Monarch is looking for her husband, who's mysteriously gone missing, and the Venture Brothers travel universes to rescue him before she catches them, thinking them to be the culprits.
But there's a lot of stuff happening at once. So if you're interested in the long version....
Most of the story takes place after the events of the movie. Dr. Ms The Monarch (who ill just call Sheila henceforth because Yeah) is still an instrumental member of the Council of 13/The Guild when the Monarch and 21 go missing one random day. Trying to balance her personal life with her professional duties, she decides to utilize her position in the Guild to get him back home.
One pet theory she has is that the Ventures have something to do with the disappearance, but obviously they are very protected on many fronts. So her solution is to have a relatively unknown and low-ranked member of the Guild to infiltrate and get information from the Ventures. She has an undercover assassin (named Kennel) keep tabs on Rusty and allows young up-and-coming werewolf supervillain Coyote to pick any other Venture to spy on as his first mission. He picks Dean, since he lives away from everyone else at college and therefore would be easier to spy on.
It gets a little self indulgent here because Yeah but Dean and Coyote hit it off pretty quickly despite Coyote's weird demeanor and they become friends, which isnt something Coyote has experienced before, at least not with someone his age. He continuously has to remind himself that this is supposed to be a no-strings-attached spy mission. Typical fluffy stuff.
In the meantime, Sheila isn't having any luck proving the Ventures to be attached to the Monarchs disappearance, and she's begun to investigate herself behind the scenes. The exact location that the Monarch vanished from is pinpointed and Dean and Hank's DNA is found at the scene. Now she's totally beside herself, because she didn't take the boys to be the type to hold someone for ransom, but all evidence is suggesting otherwise. In her mind, Coyote's mission (which he's been effectively procrastinating on) has become infinitely important, and Dean is the main suspect.
Sheila isn't stupid, and she knows that Coyote has made friends with the enemy. She doesn't mind this on it's own but she emphasizes to him the importance of the mission and how the friendship is compromising it. At this point, the stress is worn clearly on her face and she is beginning to lose her bearings a bit. Coyote leaves her thinking shes gotten through to him, but he has no intention of moving foward with anything out of fear that he would lose his only real friend if he admitted he was using him at first.
A few weeks pass of nothing else happening in the way of this investigation. Coyote is instead trying to distance himself from the Guild entirely so he can avoid having any responsibility here, but he can't bear to just fall of the map without at least asking Dean to come with him, so he starts formulating a plan to ask him if they could run away together.
AWESOME OC LORE TIME! (Sorry i promise its relevant...) Coyote is a werewolf and has been basically used as a guard dog/living weapon by the Guild his entire life. It was in the walls of Meteor Majeure that he was bitten by a dog-turned science expirement and granted his powers. After hours of tests and trials he was given a chip in the nape of his neck which can be directly controlled to keep the wolf form at bay. It's been on the same settings for a long time, and so Coyote is basically in full control of when he transforms (with some caveats.)
By this point Shiela is totally frazzled and just wants to find the Monarch by any means necessary. When she learns that Coyote directly lied to her and plans on foregoing the mission, she's furious and storms around ranting and raving about the situation to the rest of the Council, frustrated that they don't seem to care as much as she does. Watch & Ward overhear this and are basically like, "don't we have a way to directly control this guy?" Somehow they've come into possession of Coyote's remote, but they bicker over what they should do with it and it ends up broken, rendering the device totally useless and allowing Coyote's powers to spiral out of control.
This is on the same night (a full moon, no less) that Coyote plans on asking Dean to leave with him. When the remote breaks, he's already transformed willingly in order to sneak around the woods tracing the Venture's property. He runs into Hank and Dermott instead, who are dicking around outside, and Hank is quick to greet him as they've also become pals and he hasn't seen Coyote in a while. Because he can't control himself anymore, he ends up seriously wounding Hank and he has to be taken down with several darts and help from Brock and Shore Leave.
While he's out, the entire plan comes to light and Dean is obviously shocked about it. He also assumes that Coyote was killed instead of tranquilized and he starts a messy, angry grieving process that feeds into his already rebellious nature. Neither Coyote nor Dean know about the chip in Coyote's neck, so Coyote is extremely confused and distressed as to why that happened, and Dean believes that the attack on Hank was an intentional attempt at murder as part of his evil plan. Speaking of, Hank makes a full recovery but he's missing an eye now so he has to spend a lot of time doing some physical therapy stuff.
Feeling completely lost at this point Dean decides that it couldn't possibly hurt any more if he reached out to one of his only other friends, Triana. (instead of Jared, yes... trust there's a reason for this) Since moving away she's been studying interdimensional magic and out of curiosity she has Dean take her to where the Monarch was last seen and she determines that there's a huge amount of magic left behind, meaning it's likely that the Monarch somehow ended up in another universe (or at least in between them.) Dean becomes determined to continue uncovering this mystery and of course Hank wants to help.
Using Triana's magic, the Venture brothers (lol) are able to traverse dimensions. I'll call this second universe Upsilon.
In Upsilon, Rusty Venture ran away from home at a young age after growing fed up with his father. Jonas Sr ended up keeping this universe's Monarch (here he's just Malcom) as a replacement for his lost son, considering he's a clone and all. The Rusty Venture Show continued with Malcom in his place, but the show's ratings tanked because Malcom was infinitely more defiant somehow than Rusty ever was. Meanwhile Rusty only grew more resentful at seeing himself be so easily replaced by his family, and he fell deeper into hate.
As a young adult, while Malcom attended college, Rusty was caught trying to steal blueprints from his father's house in hopes of making a quick profit off of them. Jonas Sr is eerily chipper during the encounter and invites Rusty aboard the Gargantua-1 so that they could reconnect during movie night. Rusty ends up pulling the lever that would kill most everyone on board, and when Team Venture shows up, he pretends to be distraught and scared about the whole situation. Using this feigned trauma, he's able to get most of Jonas' inheritance, leaving Malcom with next to nothing and effectively sealing their disdain for one another permanently.
One of the blueprints that Rusty ended up with was a half-finished design for an artificial womb which he would use to create the original Hank and Dean. His intention originally is to have proper heirs to his newfound fortune, but he finds himself wanting to be a proper parent as they grow up, which is a feeling he is completely unfamiliar with up until this point. Despite being a frankly terrible parent, the original Hank and Dean last for 8 years. Rusty takes this as a sign that he was always meant to be carelessly evil, and that the universe never wanted him to have good things. He turns his depression into animosity and adopts his supervillain persona Dr. Monarch. Instead of hiring henchmen, he uses countless clones of his sons, none of which he holds attachment to because unlike canon Rusty, he doesn't see them as the same people, merely cheap copies of them. They haven't had the chance to grow up and are all very fundamentally similar to how the brothers are in the early seasons.
The twins from the first Universe are told by Triana that she is the only one who can communicate with them while they're in Upsilon, which explains why the Monarch has been radio silent since his disappearance. Hank is seriously weirded out by all of their clones, all wearing a younger version of his face and all missing the sparkle in their eyes. Dean is more unnerved by Dr. Monarch himself, and the way his life seems to have gone wrong in every possible direction.
They discover that Dr. Monarch has kidnapped the Monarch from his home dimension using an invention he keeps underneath his compound. He admits that he isn't sure what he wants to do with him yet, because his target was actually Rusty Venture. Dr Monarch is so full of himself, so incredibly vain in every sense of the word, that he believes that the only person worthy of being his arch rival is himself. His plan was to replace the Monarch in the canon universe and destroy his machine behind him, leaving the Monarch stuck with the mess he's made in his wake.
He offers Dean and Hank power if they come back with him and work underneath him as his right hand men. He reminds them that he's much more competent than their father back home, and that everything he promises will come true as long as they follow him. Hank refuses outright but Dean chews on the question for a while. In his mind, the world has already been turned on it's head, so why shouldn't he be a supervillain? Maybe that's what he's been missing. Dr. Monarch smugly thinks he has him beat and allows him to answer the next day, as they're captured anyway, and he's certain of what Dean's answer will be.
While in neighboring jail-cells, The Monarch says that 21 actually followed right him to Upsilon, but got sidetracked, and not even he knows where 21 could be.
Dean tells Triana the situation via a communicator and she tells him that she can't just yank them back from their current position, nor can she go in after them because the connection between universes could be severed due to her relatively novice skills in magic. So someone else would have to be sent in instead. The twins discuss who would be the best option.
They rule out most of the people they know for one reason or another until Hank suggests Coyote. Dean, confused and assuming Hank to be suffering from memory loss, reminds him that Coyote is dead, to which Hank reveals that he's texted Coyote a few times post-incident, proving him to be alive. Dean is incredibly hurt and upset at this information because he wasn't even contacted once. It only helps slightly when Hank admits he had to pester any kind of response out of Coyote in the first place. Hank only knows that he's alive because he made Brock answer him honestly back when he first woke in the hospital. Dean more heavily considers the swap to villainy, growing increasingly more snippy and passive-aggressive upon learning this, but regardless Coyote seems to be their only hope, so Triana promises to try and get ahold of him.
She considers her options but eventually figures the easiest way to get into contact with a member of the OSI is through Brock, who doesn't really know her and may not even recognize her anymore. So to not risk the mission she starts at the easiest lead, which turns out to be Dermott, much to her chagrin. The both of them work to convince Brock to temporarily allow Coyote leave from detainment for this mission. He tries to avoid it at first-- why not send him, or the OSI in general? Triana uses her magic to foresee the outcomes of this, and it becomes clear that Dr. Monarch would be expecting something like that. He has thousands of dollars in super weapons that he made himself, and an endless army of soldiers at his disposal. Brock reluctantly agrees, partially because he knows Coyote is/was friends with the twins, but decides he'd go in himself eventually if things weren't going the way he wanted.
So Coyote is released from his cell and given a rundown of what was happening and what he needed to do. He takes the assignment, eager to leave OSI custody asap, but he's endlessly anxious about his inevitable face to face with Dean after so long of playing dead.
When he gets to the edge of the property, watching all the clones gather like drones around every entrance, he almost turns around, but he winds up running directly into 21, who's also coincidentally on a rescue mission. Coyote is forced to identify himself since 21s already fired up and ready to infiltrate. Coyote tells him everything, but ends by saying he's not going to do it because he's afraid, something he's never admitted to before. 21 tells a personal anecdote, that when he got to Upsilon he couldn't stop wondering if 24 was still alive in this world. He had left the Monarchs side for what was supposed to be a brief moment, but became it's own desperate side quest.
It turns out that 24 was alive here, but he didn't know 21, so he was forced to let him walk away with very few words between them. 21 admits that he thought he'd gotten over his death a long time ago, but the feeling never truly went away. He guesses that grieving is just weird like that, "but man, does it kick my ass sometimes!"
Then he continues, conceding that the past is over and done with and all he can do is move forward. He realized that instead of living for what once was, he should live for and protect what he has now, something he feels he didn't understand when 24 was alive but he has the power to do now. This seems to change Coyote's mind, and he becomes newly determined to save Hank and Dean instead of letting their relationships atrophy out of shame and fear. 21 and Coyote work together to infiltrate Dr. Monarch's compound and rescue their loved ones. 21 suggests planting explosives around the place and Coyote, having a bit of a penchant for chaos himself, helps him.
The job doesn't go as smoothly as originally intended. They're seen and attacked by a group of the clones and have to spend a lot of time and energy fighting them off. At one point, Coyote has to transform again, although he really doesn't want to and hasn't for several months since the last incident, but it helps them out of their trouble.
At the same time, in the canon universe, Sheila is at her wits end, with no sign of her husband or 21 and all of her leads gone cold or vanished she focuses on Rusty, banding together with many Guild villains to hunt him down herself. Brock wants to go into Upsilon like he said he would, but he quickly gets occupied with protecting Rusty instead. The time 21 and Coyote have to make it back home is shrinking rapidly- if they don't get there quickly, Sheila could do something she regrets.
Hank and Dean help to put more explosives around the building while the Monarch finally confronts his doppelgänger, fighting him fist-to-fist while Coyote and 21 continue fighting off the clones. The Monarch wins his fight after kicking Dr. Monarch into one of the mounted explosives and causing it to start beeping. 21 helps Hank and the Monarch onto Coyote's back so they can hightail it out of there before the bomb goes off, but Dean is hesitant even despite the other three yelling at him to just get on. Triana pulls them back home just as they escape the firey blaze inside the building and they all end up in a heap outside VenTech tower, right in between Brock and Sheila.
Everyone is finally able to reconvene, sharing their hugs and relief with one another. Sheila apologizes for losing her mind a bit. Coyote tries to slip away but Dean follows him to talk. Dean expresses his hurt, but admits that he doesn't want it to feel that way forever, because he's seen what happens to someone when they wallow in self pity for so long it eats them up inside. Coyote says that he was scared and ashamed after what had happened, and he wasnt sure if Dean would even want to talk to him after everything. That he tried to ignore Hank too but he was so hopped up on morphine at the time that he didn't have any reservations about calling until he finally picked up. They have a little laugh about it and their relationship finally starts to kindle once more.
Sheila is so grateful to the boys that she offers Coyote a higher rank in the guild, and reminds Dean that he could technically claim his spot as Sovereign, if he would like to. Both of them almost immediately respond with a "no thanks." Hank invites Coyote in so he can help tell the story to Brock and Rusty over dinner. Blablabla cute stuff yay everything's Fun and cool ok !!!
