In Agents of SHIELD Season 2,

Episode 22 ("SOS Part Two"), Grant Ward is shown taking over Hydra, with a couple goons giving him their allegiance.

Then, in Ant-Man,

former SHIELD bigshot Mitch Carson is revealed to be a Hydra agent, and it is assumed that he has been for some time. He's clearly more of a power broker than a former specialist with a couple goofy henchmen. Also, it's unclear what he could do with the Yellowjacket serum without a team of researchers behind him, so he's probably not a lone wolf.

What's going on here? What's the status of Hydra and who is in charge?

  • Aren't the MCU and Agents of SHIELD separate/parallel universes? Specifically, Coulson is dead in the movie universe so he's clearly not running SHIELD. I know that doesn't directly apply, but the point is that just because Ward is running Hydra in AoS doesn't mean he is in Ant-Man. I feel like the two universes should have diverged quickly once Hydra became active and Coulson wasn't in the fight. – Robert Wertz Jul 17 '15 at 16:33
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    Nope, that was just something silly Joss Whedon said. SHIELD is canon. – DSL Jul 17 '15 at 16:34
  • Good to know, I know he had said that multiple times but I guess he isn't sole wielder of canon. Hopefully Coulson will return soon! Also, it's probably just that Hydra still operates in cells to prevent anyone being able to break under interrogation and ruin large amounts of work. Ward might be in charge of the main cell SHIELD is fighting against but it's still perfectly reasonable to assume there are other cells not in the fight against SHIELD, or even still in stealth mode. – Robert Wertz Jul 17 '15 at 16:39
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    @RobertWertz They're the same universe, but Coulson is just considered to be dead in the movies so people who haven't watched Agents of SHIELD, but have seen the first Avengers movie, aren't left wondering why a character who died is suddenly alive again. – Anthony Grist Jul 19 '15 at 10:14

TL;DR: It's quite likely that there are multiple HYDRA factions at this point.

By the events of Ant-Man, HYDRA is pretty fractured with most of their real leaders gone. Their de-facto leader had been Baron von Strucker, who was

killed by Ultron in Avengers: Age of Ultron.

There are most likely several different factions of the group by this point, with only one faction being led by Grant Ward. It's entirely possible that Carson is leading his own faction, or failing that, currently reports to Ward. Knowing HYDRA, he probably wants the Pym formula so that he can unite the factions and/or overthrow Ward to lead the group himself. But that's speculation.

Note: On a side note, it's important to note that Marvel's current live-action shows - including Agents of SHIELD - are indeed a part of the MCU. Coulson's death is a unique case, since it is considered an in-universe secret to most characters.

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Whoever can wrest power and hold it is in charge of whatever they can claim and call Hydra. That is the way the organization has always worked. Think of it as a terrorist organization with powerful and often autonomous sleeper cells.

"Cut off one head and two will take their place," is the axiom of Hydra because it is formed of such powerful and often charismatic individuals that upon defeat, they will go out and recruit new members to their new Hydra faction, like

Ward did at the end of Agents of Shield. He will claim himself a legitimate faction of Hydra until someone stronger can control him or he will absorb smaller and weaker factions into his own.

  • In the Marvel Cinematic Universe, we are seeing the beginnings of the splinter effect that has made Hydra almost impossible to stop after four decades. Hydra has agents who hide and fight completely from the sidelines and others to are offensive agents who attack their enemies and their projects directly.

  • If two Hydra factions can agree to work together, they combine their resources and can perform even greater feats of villainy. Baron Strucker and Madame Hydra (Viper) were known and successful collaborators.

In the canon Comic Universe, Earth-616

  • Hydra is a world-wide subversive organization dedicated to global domination. At its height, Hydra was the most extensive, powerful, and dangerous such organization in history. Hydra is almost entirely composed of men, with some notable exceptions, such as former member Lara Brown, the daughter of a Supreme Hydra, and so-called Madame Hydra, who later became known as the Viper.

  • Hydra agents wear green costumes with cowls concealing the entire head except for the mouth and chin. Their organization takes its name from the many-headed serpent-like monster known for its ability to grow two heads immediately to replace any head that was severed. Hydra prides itself on its ability to regroup and rebuild itself, allegedly mightier than before, after any major defeat. Indeed, the organization has now endured for four decades.

  • Hydra has never since achieved the power it has under Strucker. The bulk of the organization, including its most brilliant and capable members, was wiped out on Hydra Island. All that remained were fragments of the organization which had either been meant to hide out from the Spore in smaller shelters, or had been left to their fate.

  • Those who arose to lead the various Hydra factions were usually mediocrities, each of whom pretentiously referred to himself as Supreme Hydra. A.I.M. seceded from Hydra, and the Secret Empire was later revived independently from Hydra. The remnant of Hydra in New York City area was led by first by Madame Hydra, and then by the Grim Reaper and Space Phantom. A western European faction was led by Count Otto Vermis.

  • Another Hydra remnant centered in Las Vegas came under the control of the Red Skull, who managed it through the Kingpin and his son, although neither knew of the Skull’s role. Since Strucker’s demise, however, there has not yet been a leader of sufficient skill and power to return Hydra to greatness.

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