WARNING: This article contains major spoilers for "Alien Commies From the Future!", the latest Agents of S.H.I.E.L.D. episode.
Agents of S.H.I.E.L.D.'s latest episode suggests Daniel Sousa knew that Hydra had infiltrated the organization.
In "Alien Commies From the Future!", Director Alphonso "Mack" Mackenzie and his team ran afoul of Sousa when he visited Area 51 to observe a field test. He quickly detained Phil Coulson and Jemma Simmons, who were masquerading under false identities, then found himself confronted by Daisy "Quake" Johnson, who claimed to be working with the CIA.
After storming into his office, Sousa found Daisy sitting at his desk. He demanded to know who she was, so she produced some fake CIA credentials for him. He moved to call CIA headquarters to confirm this, but she managed to sway him away from that by explaining -- in detail -- how Coulson and Simmons had infiltrated the base.
"Why are you really here?" he asked under his breath. "Is this about the report I sent you guys?"
Daisy paused, thinking. "I can neither confirm nor deny that," she replied.
"Well, I hope so," he said. "Because if S.H.I.E.L.D. has been infiltrated with sleepers post-World War II, we need to root it out right now, before it takes hold."
"Look, all I can say is that you are not crazy," she told him. "And the people that you have locked up might be the key to proving it."
Of course, Daisy gave him a half-truth; after all, she was working with Coulson and Simmons all along. However, their conversation is enlightening. It proves that not only did he suspect that S.H.I.E.L.D. had been infiltrated, but that he had taken action on it. Worse still, his suspicions were right all along, and it seems like the CIA couldn't -- or perhaps wouldn't -- help.
This, of course, all loops back to Captain America: The Winter Soldier. The 2014 film revealed Hydra had infiltrated S.H.I.E.L.D. in its early days, following WWII. Arnim Zola revealed this to Steve Rogers and Natasha Romanoff, who went on to expose the ugly truth at the end of the movie. This impacted Agents of S.H.I.E.L.D. in a major way; in the Season 1 episode "Turn, Turn, Turn," the entire organization was dismantled before the team's eyes, and they have been rebuilding it ever since then.
It is unclear if Daisy will do anything with this information, like telling Sousa where and when to look for concrete proof of Hydra's infiltration. After all, she took matters into her own hands when she found out Freddy was Wilfred Malick, the father of future Hydra leader Gideon Malick, and ordered Deke to shoot him. Deke never got the chance, but her actions led to a serious rebuke from Mack and some of the others, as that would have played right into the Chronicom's plans to unravel S.H.I.E.L.D.
Agents of S.H.I.E.L.D.'s final season airs Wednesdays at 10 pm ET/PT on ABC. The series stars Ming-Na Wen, Chloe Bennet, Henry Simmons, Iain De Caestecker, Natalia Cordova-Buckley, Elizabeth Henstridge and Clark Gregg.