The movie would open with nightmarish flashbacks to a scene of a monstrous shadowed figure in a lab attacking a military woman. Quick flashes show several other scientists and guards' bodies strewn on the floor, and the woman being swallowed by flames as it is revealed it is Ellen Brandt. Her screams cut to silence as we switch to the scene outside the bar, in Iron Man 3, and we close-up on her now scarred face walking down the street where she bumps into Tony Stark. After the two part ways, instead of following Tony like in IM3, we follow Ellen. She goes to her car to gather some things, before returning to the bar to confront Tony, as she did in IM3. From here we follow the fight from Iron Man 3, but instead whenever the camera follows Tony, we again follow Ellen. The fight moves into the diner, and Tony eventually blows her up into the powerlines. We see her eyes close and the screen fade to black. We fade back into the scene after Tony has fought Savin and left, and it is revealed that the viewers are watching Ellen as a figure from the shadows, not just as the camera and audience. A monstrous shadowed figure steps out from hiding and gently retrieves Brandt's lifeless body off the powerlines.
Starting with just shots of his hand/partial body, etc., we eventually get a full reveal of Man-Thing as he bathes Brandt in the magical waters of his swamp, bringing her back to life, and nursing her back to health. She lives with him in his swamp for a few years, a shell of herself, not remembering her past. Finally her consciousness starts piecing itself back together, and she sneaks out to the heart of the swamp where Man-Thing brought her back, compelled to it. She sinks into the water and closes her eyes.
Cut to Man-Thing pulling a half-drowned Ellen out of the water. She is alert, but terrified and weak; her memory restored, but confused as to where she is and what's going on. Ellen listens as Man-Thing tries to explain. Man-Thing (Ted Sallis) lost much of his intelligence, control, and even sentience after his transformation years ago. For years, memories would come back fleetingly, and then would be lost again, mirrored by increased phenomena in his swamp. Sometimes he would be aware of who he is, sometimes not. And then, one day, in a bout of consciousness, he remembered not just himself, but his wife, Ellen. He remembered what happened to her and their unborn child she was carrying.
Cue origin story recap. Ted, a scientist was working for a S.H.I.E.L.D. research team, where he met Ellen, part of the project on the Army's side. Ted was attempting to make a Super Soldier Serum, and Ellen was there, unbeknownst to Ted, to gather data and research as part of the Armed Forces' Project Rebirth that was also secretly using Bruce Banner's research behind his back as well. After Banner's accident and the reveal of Project Rebirth's existence, Ted's research with S.H.I.E.L.D. is shut down due to concerns. Ellen and her team betray Ted and S.H.I.E.L.D. and attempt to steal his research before it can be taken away. She lied, telling him she would protect him and his research, before leading him into an ambush, claiming she "had no choice". She further threatens Ted, telling him that her cell's mission was to execute him if he was not willing to cooperate and give them the research, and that she volunteered to be the one to lead the mission, because if it wasn't her it would just be someone else who would not care if he lived. Ted refused and barely escapes, fleeing in a car with the only existing sample of his serum. While fleeing, he injected the serum into himself in desperation of all of his work being for nothing, causing his car to crash into a swamp. He should have died, but the magical energies of the swamp combined with the serum cause him to transform him into the hideous creature. His intelligence and control rapidly fading, he returned to the lab only to face Ellen and her team ransacking it, leading him to attack them.
Memories coming back to her now, Ellen remembers when she woke up after Ted attacked her in the lab. Her face was left scarred from fire and acid, and she lost her lower left arm. Her career was done and her life as she knew it was over. That is, until A.I.M. approached her to take part in the Extremis program. It healed her, but made her lose control and lust for blood and violence. The only thing she had heard about Ted was that he was alive and under "S.H.I.E.L.D. protection", to stop another Hulk/Abomination catastrophe from happening. Their child was lost in the attack in the lab.
[I chose to use this origin largely because of the opportunities to have cameos and make small connections to the universe as a whole - reflecting Man-Thing's interconnected-ness with the universe as a whole, which we learn of later. This origin specifically allows cameo of Tony Stark, mention of Captain America's super soldier serum, Ted working on the sister project to Bruce's gamma experiments, and cameos of Mockingbird (in the comics, Barbara Morse was a colleague/work-friend of Ted's at S.H.I.E.L.D.) and Maria Hill (in Agents of SHIELD, Hill implies she knows well about Man-Thing and his story so far, maybe even personally).]
With the renewed guilt and sadness of betraying Ted and losing her child, this is all too much for Ellen, and deciding there is nothing she can do for Ted and wanting nothing to do with him, she gets up to leave, But he won't let her. She cannot leave. His consciousness has only gotten clearer since he found her again. He is the closest to human he has been in a decade. So she stays, unwillingly, but also out of guilt. Time passes until finally she's planned a way-out from her captor, who she has warmed up to, yet cannot stay with. As she opens the front door, a figure is standing there.
Recent dimensional travel (Ant-Man, Doctor Strange, Avengers: Engame) has stressed and shattered the Nexus of All Realities, a cross-dimensional gateway which provides a pathway to any and all possible realities that happens to be in Man-Thing's swamp [hence the phenomena Man-Thing had been noticing and his connection to them]. Dr. Strange has come to help Man-Thing restore it. [This is a direct storyline from the comics, and can be altered from here.] Man-Thing's transformation did not happen by chance. He was selected by the Nexus to be its Guardian. It is his duty to protect the doorways between worlds from being opened, but as the Nexus has been shattered by measures he could not control, the fragments of the Nexus must now be gathered from across space and across realities.
[In the comics, Man-Thing was possessed by K'ad-Mon, the history of the Men of Lineage was revealed, and Sallis learned that his relation with Ellen was predestined to restore his hereditary mission. Ellen, the Man-Thing, and K'ad-Mon [and Dr. Strange in our movie] recovered Nexus fragments from various places, including a Nexus-created planet that Ellen had to destroy in order to save reality. The gang even recovered a fragment from our good ol' Guardians of the Galaxy star, Howard the Duck...]
[This may be a lot for one movie and so we can leave the shattering of the Nexus and dimension hopping for Movie 2 +, and have Movie 1 focus on the Nexus being "disrupted", Dr. Strange coming to investigate the strange anomalies and phenomena, and Man-Thing having to save "just" Earth (instead of realities) from an invader.]
In the second half of our movie, we instead have Man-Thing and friends fight Thog the Ancient and his demons, who cross out of the Nexus and threaten to open the passage from Earth to his nether world, and wreak havoc. Before the final confrontation, Man-Thing and Strange discover the reason why Thog was able to get through was because of the missing fragments, forcing Strange to leave to figure out what's going on, leaving Man-Thing and Ellen to fight Thog alone, and opening up the door for the future dimension hopping movies.
The great thing about making a series of Man-Thing movies means even more connections. Man-Thing has worked alongside the Hulk and Thor in the comics, and has reason to team up with them later on. In fact, if we want, we could even bring in Erik Selvig, who stumbled upon the Nexus of Realities while studying the convergences of the Nine Realms. Jennifer Kale/Atlantis, Ghost Rider, Midnight Sons... there are a lot of tie-in possibilities.
But here is the best part about the Man-Thing and the Nexus of All Realities. After the Infinity Stones story is complete, we could easily twist the Nexus of All Realities to create an "Incursions" type story line. "Cross-dimensional gateway open to all possible realities" easily equals "alternate reality heroes attacking our heroes", "villains reimagined as heroes in their reality", etc. We got a whole half a phase at least there.
Multiple realities would also create an internal consistency and precedent for a Spider-Verse arc down the road, or allow you to do movies that couldn't practically exist in the normal MCU reality *cough* Marvel Zombies *cough*.