Exclusive: How 'Secret Empire' will shake the Marvel Universe to its core

— -- The Avengers, X-Men, Defenders, Inhumans, Spider-Man, and more, united against … Captain America!?

After the events of "Civil War 2," the Marvel Universe's biggest and brightest superheroes are reeling at best. Things are about to get a lot worse.

Bruce Banner (Incredible Hulk) and James Rhodes (War Machine) are lost and the incomparable Tony Stark is in some kind of coma, passing off the mantle of Iron Man to Riri Williams. All while superheroes like Captain Marvel will have to deal with the repercussions of their actions in the series, which rolled out late last year.

It's kind of a mess and that's where Captain America steps in. Everything changed last May for the formerly squeaky clean icon when it was revealed he was actually a Hydra agent, the nefarious underworld organization he had been fighting against for the last 70 years.

With this Earth-shattering news still fresh in the beleaguered minds of die-hard Cap fans, the question is where do they go from here? Enter Marvel's new series "Secret Empire," where everything is about to change, not just for Captain America, but for absolutely every hero in the Marvel Universe.

ABC News exclusively spoke with Marvel's Senior Vice President Tom Brevoort and Editor-in-Chief Axel Alonso about the recent past, the present and the future of Marvel Comics.

Hydra?!

After Steve Rogers had his super soldier serum neutralized a few years back, he could no longer be Captain America. Sam Wilson, the Falcon and Steve's best friend, stepped in until a character named Kobik, a living cosmic cube, used its powers to bring him back, with one unknown caveat.

"Unbeknownst to anybody but the readers, when Kobik did this thing to Cap, she had been influenced by the Red Skull [his archenemy dating back to WWII]," Brevoort explained to ABC News. "She didn't just restore Steve, but changed his history, so that he had been a Hydra operative and true believer going back to his earliest days as a young man in the 1920's and 1930's."

When that was revealed in "Captain America: Steve Rogers #1," everyone lost their minds. Even the actor Chris Evans, who plays Cap in the Marvel Cinematic Universe, tweeted his confusion and frustration. "Hydra?!?!? #sayitaintso," he wrote.

"It's a pretty juicy turn of events," Brevoort said. "This character, who is the most respected, the moral compass of the Marvel Universe ... is secretly a viper in the nest?!"

Fast forward to a post "Civil War 2" universe and, while the readers know, those in the Marvel Universe are blissfully unaware of Cap's true motives and ties. But, that's all about to change.

"Every time there's a scene with Steve Rogers, it takes on two levels of meaning," Brevoort added. "There's the surface of whatever's going on, whatever bad guy Cap and Spider-Man are punching and there's this secondary level, like what's he really doing? 'OMG, Spidey, be careful, that guy's actually a bad guy!'"

Secret Empire

This highly-anticipated series -- written by Nick Spencer, with cover art by Mark Brooks and rotating interior art by Steve McNiven, Andrea Sorrentino, Daniel Acuña, and Leinil Francis Yu -- will be the culmination and unresolved turn of events from that shocking story, Brevoort explains. But like all Marvel books, there's no guarantee it will be wrapped up in any "neat, tidy bow" for the readers after its 9-issue run.

"Steve has been kind of lining his dominoes up around the Marvel Universe to be able to make his move and bring about a Hydra revolution, a takeover," Brevoort said. "At the point of 'Secret Empire,' they are ready to go. That's the moment we hit as we go in."

Cap will be unmasked as a Hydra agent pretty early on.

"His plans and Hydra's plans will have begun to unfurl," Brevoort continued. "We are done with the covert portion, the buildup portion of the program, 'Secret Empire' is the pyrotechnics, the big Michael Bay blockbuster, huge colossal struggles and battles across the Marvel Universe, with all of our key characters and players taking on a big role."

In issue #0 (April), it's effectively, as Brevoort puts it, "the worst day of the Marvel Universe."

"Where not one, not two, but three separate events break out all at once. Cap, as head of S.H.I.E.L.D., is able to mobilize forces to all three of those situations. And those three situations represent Hydra's first move. It comes off the blocks explosively right from the get-go," he added.

By issue #1 (May), the Marvel world knows who Rogers really is.

"If you are going into this story not knowing how it's going to go, yeah you should have some misgiving about [a happy ending], because it's a really ridiculously awful situation he is in," Brevoort said. "It might not all be fine."

All the characters close to Cap will be touched by this, but the Marvel masterminds stress that "everyone" will be affected by this.

"We'll definitely see an impact on our new, younger generation of heroes, a huge turn for them, a Watergate moment for them," Brevoort said.

"They will have to grapple with what this means and reset their heroism," he added. "You don't want it to be bleak and miserable, you always want to have hope and be uplifting, and that's the aspect of this story where the other characters in the Marvel Universe have to kind of come together for."

Alonso said, while Cap is the nucleus of this story, "this story is going to be told through the perspective of multiple characters, who are dealing with the threat this poses."

"Some roles and characters will come to the foreground at different moments in the story and play a big role in saving the day," the Editor-in-Chief added.

The Future of The Marvel Universe

What the team at Marvel wants out of this conflict is a newly united universe once again, something fans haven't seen in quite some time.

"We've just come off of 'Civil War 2' and 'Inhumans vs. X-Men,' two big, dark events that had heroes fighting against heroes, over somewhat defensible positions. This is very much more an old school story. You will know who the good guys are and who the bad guys are. This is not heroes fighting heroes, this is heroes fighting a bad guy," Alonso said.

He continued, "We saw this moment as our chance to rally the entire Marvel Universe, which has been fragmented of late."

"We saw this as the rallying cry, where we could have everyone -- Avengers, Guardians, Defenders, X-Men, Spider-Man, Deadpool -- all rally against this thing and unify the universe into the future," Alonso said.

As with all their big storylines, "Secret Empire" was planned well in advance, the concept taking shape years prior to now.

"When we made the decision to have Cap's memory rewired, thus that he would be come a Hydra agent," Alonso said. "You would have the most trusted superhero in the Marvel Universe become a super villain. You don't do something like that without considering what a huge story it is. You understand you're teeing up a huge story and that's what this is."

"We are already planned out two or three moves beyond [an out to this story]. We are always planning a year, 18 months into the future. We know exactly how this is ending, we know what's coming after that and after the thing that's coming after the thing," Brevoort chimed in.

"Secret Empire" hits shelves nationwide with issue #0 in April, followed by issue #1 in May. The series will run until August.

Note - ABC News and Marvel are both part of parent company Disney.