Marvel's big Secret Empire event has started. This is the result of all the build for the past year or two, with Captain America as a dictator-like head of Hydra. So how did it come this?
Previously:
-The Red Skull, who was dead before, was brought back a few years ago. This version of him is cloned from as he was during WWII, so he's much more ruthless.
-The Red Skull gets a piece of the deceased Professor Xavier's brain and has it added to himself, giving him psychic powers.
-Captain America loses the super soldier-serum inside his body, which ages him to that of an 80 or 90 year old man.
-At some point, a cosmic cube is taken and given sentient life as a
magical little girl named Kobik. Yes, really.
-Said magical little girl's cosmic cube powers are used to create a new kind of supervillain prison by Maria Hill and SHIELD. It's a small town where everything seems like it's out of a 1950s sitcom. The villains are changed to think that they are regular people.
-Some of the villains realize they have been mind-fucked and plot to change things back to normal. They succeed.
-At some point, The Red Skull 'befriends' Kobik and makes her think that it will help Captain America if she fucks with his mind.
-During the event where the villains are getting their memories back and breaking out of the prison-town, Kobik restores Captain America back to his youthful self. It is at this point that his memories (and it appears, part of reality along with them) get altered.
-Steve's memories of the past are now that he was recruited by Hydra and trained to be a spy by them. He still becomes Captain America, but is secretly working for Hydra.
-Hydra are not the Nazis and have different goals/beliefs during this time.
-Present-day Steve is now working for the Red Skull, secretly, and
doing thangs behind the scenes to further the Hydra agenda, including killing people outright. Meanwhile, the Red Skull is building up the Hydra ranks.
-However, Steve has his own agenda. He is told to kill Dr. Erik Selvig, but instead hides him away in a safe house.
-Kobik has been hid away and 'protected' by the Thunderbolts, who were led by The Winter Soldier. During this series, she attempts to alter Bucky's past as well, but fails.
Secret Empire stuff:
-In Uncanny Avengers, the Red Skull is defeated and Beast operates on his brain to remove the psychic abilities.
-At the end of the current Thunderbolts run, Baron Zemo pops up with some villains and gets some Thunderbolts to turn villain again.
-They beat the shit out of Bucky and Kobik is 'killed'. She turns back into the cosmic cube and shards fly all over the place.
-Bucky is tied to a plane, with a bomb, and sent out into the sky to die. The plane explodes and
this being a comic book, he's probably still alive or will come back.-Dr. Selvig, who (I guess?) created Kobik, does something that helps her to turn back into
magical little girl again, then kills himself.
Uh?-Steve has continued
doing thangs and has set himself up to become the supreme commander of SHIELD. He purposefully gets the alien Chitauri to come invade Earth.
-In space, Alpha Flight, led by Captain Marvel, protect Earth from threats and also have a giant planet-spanning barrier shield up. This is disabled by what appears to be a suicide bomber from Hydra, but is really Steve fucking with them. He re-activates the the shield and cuts off Earth from everyone in space, effectively locking out Alpha Flight, Captain Marvel, and The Guardians Of The Galaxy. And the Chitauri are still around.
-Steve confronts The Red Skull, reveals that he's not working for him anymore, and throws him out a window onto some rocks, killing him.
-Steve is given full power over the military because of all the shit going on and then reveals himself as the new supreme leader of Hydra.
*Whew*
Now for the dumbest part of this- The Kobik-altered past of Captain America is made further fucked-up when it is revealed that Steve was originally an agent of Hydra, trained since childhood, and that the Nazis won World War II. What changed things is that the Americans found the cosmic cube and used it to alter reality to win the war, making Steve think that he was a good guy. Steve, back in the WWII era, is taken to a super-duper-secret Hydra stronghold in Japan and shown visions of all of this and the 'altered' future. He is put into some magical pool that will prevent him from being completely altered and in the future he will be restored to his full-on Hydra self, which is where the story is now.
So what Marvel has done is basically retconned Captain America to have always been a super-villain from the beginning.
Comics

Rather than having gone through all that dumb shit, I don't understand why they didn't simply have The Red Skull use his psychic powers to fuck with Captain America's mind and
turn him heel. They need to keep this stuff way more simple and stop it with these convoluted messes of storylines.