After nearly two years of deception, Tony Stark finally revealed he was the "new" Iron Man in Avengers West Coast #72 (1991). Enough time had passed since the Armor Wars that the other Avengers were not outraged by his circumvention of their procedures or the overall deception - they were simply quietly disappointed in him for deceiving them. Soon afterward the entire line of Avengers comics participated in a crossover called "Operation: Galactic Storm," wherein the two extraterrestrial powers of the Kree and the Shi'ar went to war, which was a problem because their fleets were passing through Earth's solar system and endangering its sun. Captain America and Iron Man served on the team of Avengers who went to confront the Kree in the hopes of finding a diplomatic solution. However, the Kree's leader, the Supreme Intelligence, had masterminded usurping control of the Nega Bomb weapon the Shi'ar had designed and he permitted it to detonate on the Kree homeworld. Although the population had been devastated, the Supreme Intelligence had been trying for ages to jumpstart the Kree's evolution and hoped the bomb's fallout would have that effect upon the survivors.
In the aftermath, the Avengers fell into disagreement in Avengers #347 (1992), some proposing they kill the Supreme Intelligence as retribution for his actions. Captain America flatly turned this down.
"The Supreme Intelligence is a sentient being... to kill him is.. unthinkable. Let the Kree survivors handle this. The war is over.. the stargates won't be used again. Earth is safe. There's nothing more we can do. Dear God, we can't bring back the dead."
Suddenly, Iron Man fired a repulsor ray at the ground before Captain America's feet, then declared, "I'm the only original Avenger present... and I'm pulling rank, Cap." This was unprecedented; Captain America, aside from being the team's leader at the time, had been considered to be equal in stature to the founding Avengers, having joined them in their fourth issue and been more consistently present than any other Avenger. This idea that Iron Man (or any other founder) had special privileges within the group was an invention in Tony's mind - an excuse to seize power. So doing, Iron Man led Vision, Hercules, Thor, Sersi, the Black Knight and Wonder Man in executing the Supreme Intelligence (at least, so they thought - being a quasi-computer, he uploaded his consciousness to another location only pages after the execution scene). Unlike some earlier infractions, the Avengers convened on the issue immediately after in Captain America #401 (1992). The team decided not to discipline the Avengers who participated in the execution and Cap offered his resignation; no one would accept it.
Finally, Hawkeye took Steve out to a bar to try and help him work through his issues, to no avail (Steve not being much interested in drinking due to his alcoholic father). Fortunately, Tony Stark came to the bar to address he and Steve's troubled past (no small feat, given Tony's own alcoholism). The two men rehashed everything which had gone wrong between them since the Armor Wars. Tony finally apologized for not explaining himself during the Armor Wars and shirking his responsbility to his friends. Tony also offered his most heartfelt words about Steve to date:
"You're an inspiration to me, Steve. To a lot of us. We may not think like you or act like you -- but we still respect you and appreciate what you do and the way you do it. You're an idealist in a world that is far from ideal. I don't know how you can do it, Steve... how you can keep all the ugliness from getting to you... hardening you.. I can't. I'm not as perfect as you... forgive me."
Steve responded, "I appreciate how much courage it took to come here -- in a bar of all places -- and to level with me like you just did. I'm really sorry our ideological differences bent our friendship out of shape. I miss having you as my friend." And so, despite Iron Man's insubordinate and murderous behaviour, Steve and Tony came through this troubled time with their friendship stronger than it had been since the Armor Wars.
As time went on, they continued to be casually friendly with one another. In Iron Man #303 (1994) as Captain America was slowly deteriorating as his Super-Soldier Serum failed, he confided in his condition to Tony at a time when the other Avengers didn't know; it was a situation Tony could certainly respect, given his own past health troubles and need to keep secrets. Later, when Cap's health completely collapsed, Tony built a suit of armor so that Cap could continue to soldier on. Said armor was an eyesore, but it's the thought that counts.
Eventually, the Iron Man/Captain America tension had to make a comeback, this time in the Iron Man & Captain America 1998 Annual. In this story, Iron Man briefly gained access to the telepathic powers of Mentallo and decided to use it to erase his secret identity from the minds of everyone who had learned it, friends and foes alike. Afterward he went to the Avengers and unmasked before them, which instantly restored their previous memories of his secret identity. Of all the Avengers, Captain America was the one most upset by this extreme violation of people's psyche. Unfortunately, Cap voiced this displeasure primarily through bitchy, catty dialogue such as, "I decided to take him out myself. That is... if I haven't offended you by doing my own thinking." Still, they weren't allowed to be upset at each other outside of the pages of this annual. In the main plot, they discover a communal hivemind called Zenith City which Iron Man's foe MODOK is harnessing to enhance his psychic power. Iron Man resolves that the hivemind must be shut down, despite the wishes of its members. Conveniently, Iron Man's armor loses power before he can shut down the hivemind himself so Cap must perform the act. By doing so, Cap is put in Tony's shoes and reaffirms their friendship:
"I still think you overran your boundaries, Tony... that your ends didn't justify your means as neatly as you say they did... but I also think I tend to be a little judgmental sometimes... particularly when it comes to issues of independence and personal rights."
Cap's speech above neatly summarizes why the two are often in conflict; Tony's belief that the ends justify the means contrasted with Steve's belief in personal rights. Which is precisely what the Iron Man-Captain America brawl-for-it-all was about.
Tomorrow! Why is this man smiling?