Warning: contains spoilers for Captain America/Iron Man #3!
Marvel's Secret Empire event of 2017, in which Captain America revealed himself as a secret Hydra spy, received one of the worst fan receptions for a story arc in recent memory. Attacked from all sides, the story was hardly referenced in Marvel continuity, despite the world-changing events of the comic. Now in Captain America/Iron Man #3, Marvel all but admits the story was a colossal failure from the start.
In Secret Empire, Captain America reveals himself as a sleeper Hydra agent, and perhaps most shockingly, he's always been one from the start. Hydra begins to take over the world with Captain America as the face of the movement. In the end, the entire affair is revealed to be the result of the Cosmic Cube altering reality, and the real Captain America emerges to battle the Hydra-aligned Steve Rogers. The latter is soundly beaten, and Marvel did its best to put the entire event firmly in the rearview mirror and put the fascist-punching, self-sacrificing Captain America front and center once again.
But such a monumental turn of events isn't easily thrown under the bus, and in Captain America/Iron Man #2, Steve Rogers faces off against the Hydra Captain America once more - in his yellow and green Hydra armor (drastic color changes is an excellent method to signal to one's audience that a character has turned evil). In the aftermath of the fight, Iron Man senses that Rogers is troubled, and realizes that he wanted the Hydra Captain America to resist his programming. "Even though reality had been altered, you'd have expected any version of Steve Rogers to fight against fascism, wouldn't you? [And]...the armor is - what? A symbol of your failure to fight the impossible? You do realize how astonishingly dumb that is, right?" Steve brushes him off, but deep down he knows Iron Man is right, on both counts.
The entire affair strained plausibility for both readers and characters in-universe. While the Marvel Multiverse suggests the possibility of a Fascist Captain America can theoretically exist, the idea that the 616 version could be corrupted and indoctrinated so throughly into Nazi ideology was outright refused by readers. In addition, Captain America was created by Joe Simon and Jack Kirby, two Jews who had a personal stake in the entire war (thus creating Captain America even before America entered the conflict); to turn their anti-Nazi creation into a Nazi himself just for the sake of shocking readers and drumming up sales was seen as woefully distasteful.
The event was largely seen as a grand misstep, and one rarely referenced after the fact. Captain America and Iron Man have been at the center of rather contentions events in which their behavior was widely derided (Civil War for Iron Man, Secret Empire for Rogers). Captain America's legacy is, thankfully, stronger than the occasional bad story, no matter how shocking it may have seemed at the time.