The basic gist of it is this: Tony doesn't like bullies.
He doesn't like it when someone uses superior strength, or firepower, or political clout, or what-the-fuck-ever to push someone else around. To make them bend. To make them less.
This is a lesson learned in a dark, sandy cave that now lies forgotten, filled with the bones of people who'd thought Tony Stark less than them. (And if someone were to say that his arms dealing makes him a hypocrite... Well, he sells to the oppressed, too, and often at a much more reasonable price. He keeps his balances checked.)
And that is why Iron Man is committing treason. (Well, maybe not entirely. There is the other reason, the "I've seen something fantastic and I want it" reason. But he allows himself a bit of delusion, in the name of self-aggrandizement.)
See, once upon a time, there was a man. A brilliant man, who wanted to save humanity, raise it up to something better, but instead was steered to make a weapon. Was steered to make a weapon out of himself.
Tony's seen the footage, the test results. He's seen what Doctor Bruce Banner accomplished in the name of a lie, and what he was given for it. Imprisonment. Experimentation. Isolation. Dehumanization.
Bruce Banner is kept in a sterile, fluorescence-lit white cave, where he is used to make weapons for people who thinks he's less than them.
Of course Tony couldn't stand idly by.
The security measures of the compound are quite impressive, and Tony assumes they'd have to be, considering what they're supposed to keep in. Still, they're geared towards keeping a physical entity in, not to keep a non-physical entity out. "JARVIS, are you in their system yet?"
The cadence of JARVIS' voice implies vast amounts of insult. "They don't have any system but me anymore. Sir."
"Excellent. Unlock me a path," he says, and smiles behind his mask. God, he does love JARVIS.
"Already done, and I've taken the liberty of uploading you a map," JARVIS replies. "Should I disable the alarms, too?"
Tony considers. "No. Let them hear me coming."
The next few minutes are noise and explosions and fire, and Tony can't help but laugh as he tears through the compound, taking care of hopelessly outgunned soldiers and panicked scientists, and he doesn't feel a whit remorse, because frankly, they all had it coming.
Bruce Banner is kept in a cell in the very middle of the lowest level of the compound, buried under nearly a two miles of earth and concrete and every military-research-spawned alloy known to man.
When he sees him, Tony wonders why they even felt they needed to bother.
Banner is thin and pale and bruised, and sleeps the sleep of the heavily fucking sedated, strapped into a full-body straitjacket made of what Tony guesses is some new kevlar/carbon-fibre/whatever composite material, caged in a snug metal harness, and hung suspended midair to deprive him of any leverage.
Tony actually feels a bit sick.
The good doctor doesn't wake up as Tony gets him down and out of his layers and layers of kevlar, and doesn't even twitch as he's carried out of the burning building, but his eyes do finally flutter open when Tony settles him in the back of their getaway vehicle; a very, very nondescript SUV that Tony may or may not have stolen from a military storage facility.
Banner's eyes are animal and wary, even as they can't seem to focus, and his abused voice comes out a wordless growl. He brings a hand up to scrabble at Tony's armor, trying to fight or hold on or both, and Tony reacts to the burgeoning panic in his eyes by letting his faceplate slide up away from his face. "I'm not a lab tech, Doctor Banner," he says, tilting Banner's face up and making him focus on Tony's eyes. "And I'm not a soldier. They're all dead."
Banner blinks slowly, forehead pulled into a frown as he works to parse the words.
"I got you out," Tony says. "You're out. And you're not going back in."
This seems to get through the haze of Banner's thoughts, and his eyes widen, shocked and wondering, and this time his voice comes out more like actual language, something resembling maybe a "who?"
Tony gives him his very best smile. "I'm Tony Stark, your knight in shining power armor," he says. "And I'm very pleased to make your acquaintance."