Honestly, I'd adapt Armor Wars and Five Nightmares with Zeke Stane as the main antagonist and Ghost as his main henchman.
Act 1
Starts with Tony looking down upon Happy Hogan in the hospital and is informed that he won't ever recover. Tony is forced to euthanize him by taking him off life support. He's now dating a new girlfriend. An Italian supermodel named Guileta Nefaria. She jokes that her father probably wouldn't approve of Tony or other, "law and order types." Tony is informed by his new security chief Beth Cabe that there's a break in at the Stark International offices in LA. Tony immediately suits up as Iron Man and evacuates who he can while fighting off Ghost and Spymaster. The latter doesn't survive when he's crushed by debris but Ghost escapes and Guileta is injured and gets hit by exhaust in the fight between Tony and Ghost. After Ghost defeats Tony one on one and as Tony lies defeated, a man claiming to be Obediah Stane's son confronts Tony as he lies in the rubble of his collapsing offices and tells him that he's waited years to finally get his revenge and he's not only wired all of Tony Stark's assets to him but he's also downloaded the Iron Man schematics and leaked them onto the internet so ANYONE can now by Iron Man. Now a broke, homeless Tony Stark confronts Guileta in the hospital and she immediately dumps him because Tony ruined her face. Tony explains that it's an accident but Guileta doesn't want to hear it. Tony tries to move back in with Pepper and she tells him that she left him for a reason and it's what being Iron Man does to him. Namely how Tony copes with all the stress of constantly fighting supervillains with the Avengers. "It isn't the armor, Tony. It's the bottle." Tony tells her that he can stop drinking whenever he wants. He just doesn't want to and Pepper kicks him out. The only possession that Tony still has is the Iron Man armor that he was trapped in back when his corporate HQ was destroyed.
Fast forward to two months later. A homeless, drunk Tony Stark vents to a woman in a bar named Gretl Anders about how the Avengers are now bankrupt and he can't bring himself to face them anymore. She says that Tony really needs to stop being so hard on himself. He's a hero and can be again. Tony talks about how for the first time in his life, he needs a leg up and everyone who still cares about him is all the way in New York. Then he remembers that there is still one guy in the area, thanks Gretl and heads off to see Hank Pym.
Act 2
Hank mentions how he's now the man funding the Avengers and that Avengers Tower may have been sold but they're still in a mansion on 5th Avenue. Tony asks about Pym particles and Extremis. Hank mentions that he's never giving Tony Pym particles but he's let him experiment with Extremis and says that if somebody's compatible with it, it can be used as an ant-aging treatment. Tony replies with, "Hopefully I won't look like a teenager" in a nod to The Crossing and Hank says, "No. Just another 15-20 years off your life." It's confirming that Downey is going to be recast in the role and that we're also likely to see a younger Hank Pym take up the mantle of Yellowjacket. A montage ensues that shows Tony experimenting and finding that Extremis can be modified to engage in technopathy, making Tony a transhuman cyborg... assuming that Extremis doesn't make him explode. Tony says that it's a risk that's worth taking. He enters a stasis pod after injecting himself with both extremis and liquid metal and when he awakens, he's covered in cocoon. He breaks free and finds that he now can control magnetism and remotely hack into Hank's computers. He says aloud, "I can quit whenever I want..." and struggles with a bottle of whiskey in his hand, he starts trembling and eventually decides to throw the bottle at a wall to show that he's just going to quit drinking and go cold turkey. He thanks Hank and sets off on the rest of the second Act which is just one big action montage.
Tony confronts Rhodey at Avengers Mansion and mentions that his leg prosthesis comes from the same technology that powers the War Machine armor. Tony then stabs the prosthesis with a needle embedded in Tony's wrist that shuts it down. As Tony is now shown to become one with the Iron Man armor (that looks suspiciously like the mid-90s Modular armor), He starts escaping over New York while Rhodey claimbs into the War Machine armor. Tony mentions how everything else he's built has just caused misery and suffering and Iron Man is the only good thing he's brought into the world and he's now seeing the Iron Man technology used to wreak havoc across the globe. He hates having to do what he's going to but there's only enough room for one Iron Man. Tony stabs Rhodey's suit with the same needle (this time embedded in the armor's wrist) and Rhodey comes crashing down in the middle of Times Square.
Tony then sets out in a number of short battle with Beetle (who's considering calling himself Mach and gets shoved through a Gilette billboard after Tony deactivates his armor) and Controller that are both only a few lines each and a brief fight scene. The one at Hammer Industries HQ where Tony fights Justin Hammer's niece, Sasha is a bit longer. Justin Hammer's sister Justine is now running the company and has kickstarted Project Firepower. Sasha mentions how she's so happy to finally meet TOny Stark but that her uncle says that Tony's a jerk.
Tony: I'm not here to fight a little girl.
Sasha: I'm 16!
Tony: Friday? Engage Hack Protocol.
(Sasha's armor starts punching herself in the face)
Sasha: Hey, that's cheating.
Tony: If you need somebody to hit you, I think you've got that covered.
Tony stabs Shasha's suit with the needle then fights a number of guys in Firepower suits. As he flies away Sasha says, "My uncle's right! You are a jerk!"
Tony then confronts Ghost. Tony defeats Ghost by shooting electricity at just the right voltage while Ghost is intangible and then mentions that Ghost is being sent to The Raft.
Act 3
Steve confronts Tony at the old Stark warehouse that Tony's been sleeping at. He's now wearing the mid-90s Cap Armor. Steve says that Tony's been kicked out of The Avengers and that Tony's completely out of line. Tony says that he's doing what he absolutely has to do and there just wasn't another way. Tony defeats Steve and says, "It's okay. You'll live. You heal fast." He tells Steve to take good care of the Avengers and next time he sees them, if he ever sees them again, he owes both him and Rhodey.
Tony then tracks down Zeke Stane. Zeke says that he doesn't want to fight but to talk and play chess. Zeke talks about how Obediah was abusive towards him and how the most important rule his father lived by was, "always be a winner at everything you do. Failure was never an option." They discuss the nature of information, proprietary vs open source and whether or not patents stifle innovation. There's also talk of transhumanism and how both of them have become more than human through cybernetics with Tony also mentioning how he modified Extremis. Zeke says that he still has most of Tony's money that he stole and how if Tony wins in chess, he'll give it back but asks what Tony will do with it since they're both fugitives now and it isn't like Tony can get his old life back. As soon as Tony scores a checkmate, Zeke summons his armor and Tony also suits up since Zeke doesn't take failure well. Tony and Zeke battle across a small town and Zeke eventually grabs a small girl as a hostage and tells Tony to kill him or he'll kill the kid. Tony hits Zeke with a stun attack and tells Zeke that he should have left his helmet on. Tony then charges at Zeke, and when Friday informs Tony that his suit power is running low, Tony says to engage Extremis as a backup. Friday informs Tony that it might kill him and Tony says that he doens't care. Tony and Zeke fight in an empty field as the soundtrack stops and Johnny Cash's cover of Nine Inch Nails "Hurt" starts playing. Tony starts recording a monologue and the film cuts back and forth between Happy 's heart rate monitor expiring, shots of Pepper, Guiletta, Rhodey, Steve and even Ghost and Beetle in a cell together on The Raft as Tony hijacks TVs across the world to broadcast a message, "I just want you to know, that even when I've hurt you, I still loved you. All of you. I'm not ever coming back from this. It's been a ride, hasn't it? Hell, I've had the time of my life. I never imagined that I'd get the chance to be a hero, an Avenger of all things, what with Loki, Hydra, Utron... Thanos. I'm not going to lie about it being a burden but I loved being Iron Man. I just never thought about the consequences of what being Iron Man meant. I never thought that what I made to help humanity could very well wind up destroying it. This isn't the world I wanted but it's the world I built. I've ruined friendships, relationships, everything... but I'm not going to bring down humanity with me. I'm letting loose an EMP blast calibrated to just the right frequency to shut down every Iron man suit on the planet. I don't know what this new world will look like but I'm happy to be the man creating it. Good bye."
Zeke's only reply is, "What do you think you're doing?"
Tony's respoonse is, "Taking you with me. Friday, engage global Edxtremis EMP blast."
Friday: But Tony, that will.
Tony: I know.
A huge blast erupts and Pepper watches in shock and screams, "Tony! NO!"
The scene cuts back to the earth as a wave of energy covers the globe. The scene cuts back to the field and we seen Tony's helmet is all that remains. The lights remain on for a second but then fade out.
Post credits 1
Rhodey is back in a Stark warehouse and Pepper mentions that she can save the company because Tony transferred the money back shortly before his death. She also mentions that Tony wanted Rhodey to have something in case anything ever happened to him. It's a crate and inside is a new War Machine suit with a not inside that reads, "As I said. There can only be one Iron Man."
Post Credits 2
The Raft. Zeke Stane is eating lunch with Beetle and Ghost. Ghost is naturally still wearing his armor since and trying to stick his spoon up underneath it. Beetle says, "so, you still want revenge on those Avengers guys?" Zemo only replies with, "Not revenge, Justice.. Like lightning."
Next film will be War Machine: Dragon Seed since Dragon Seed Saga is the definitive War Machine story and it's a great way to get the real Mandarin to make an appearance. Plus Mandarin works better with a War Machine film since Chinese audiences absolutely hate films starring black people so it won't hurt the box office all that much if it gets banned there. Dragon Seed is where we learn that Tony faked his death (Just like he did in the comics) and the new actor is explained away as the Extremis virus de-aging him. Like I don't feel like a plot for Phase 4 where Tony fakes his death in any way would cheapen what happened the previous year since it would still be RDJ saying good bye to the role and the fans and I still feel like it would be heartfelt. Iron Man 4 would still be a film that the audience would leave in silent contemplation rather than giving it a standing ovation while the War Machine spin-off would absolutely be a feel good blockbuster. Tony's, "taking you with me" line was literally about Tony taking Zeke with him as a travel buddy and Zeke also helps defeat Fin Fang Foom and the other alien dragons in the climax. Like it needs to be a secret that Tony survived and he shouldn't even appear until the third act and be completely kept out of marketing.
Anyway, I'd cast Donald Glover as Beetle, Zac Efron as Zeke Stane and for Ghost, I really don't have anyone in mind. Controller and Justine and Sasha Hammer wouldn't appear in any future films so I'd event take a woman in the role. It's not like Ghost ever leaves the suit. Come the War Machine film, I'd cast Donnie Yen as Mandarin and recast Shiloh Fernandez as Iron Man.