Life Model Decoy/Chronicom of Phil Coulson, time-traveling throughout the 20th century history of the Marvel Cinematic Universe. The alien Chronicoms are trying to stop SHIELD from being created and they're targeting key events in the past involving Hydra, which was secretly part of SHIELD since its very inception.
Bucky Barnes AKA The Winter Soldier as Hydra's top assassin for decades. Rogers and Romanoff also learned from Arnim Zola that Hydra infested SHIELD like a virus since its creation after World War II. Working covertly from within SHIELD, Hydra manipulated world events like the Cuban Missile Crisis, the rise of Muammar Gaddafi in Libya, and the Cold War to its advantage. Shockingly, no one in SHIELD ever knew that Hydra was part of the agency since the beginning. Or almost no one.
In Captain America: The Winter Soldier, Nick Fury "noticed" something was deeply wrong within SHIELD and, 60 years earlier, so did one of his predecessors. Agents of SHIELD season 7, episode 4, "Out of the Past" teases that Daniel Sousa also realized Hydra's tentacles had a grip on SHIELD. The film noir-inspired "Out of the Past" will detail the alter the MCU's history in ways that can't be imagined.
After the events of Agent Carter, Sousa rose to become the West Coast head of SHIELD, operating out of Los Angeles. In Agents of SHIELD season 7, episode 3, "Alien Commies From The Future!", Sousa encountered Coulson and his time-traveling team, including Gemma Simmons posing as his old partner Peggy Carter, at Area 51 in 1955. SHIELD stopped the Chronicoms from destroying a prototype ion fusion reactor called Helius, but that isn't the end of Sousa's dealings with the Agents led by Coulson (who's "a big fan" of Sousa) and Agents of SHIELD will show fans how the Agent Carter hero's death affected the greater MCU.
When World War II was over, some Hydra agents fled to South America but others remained in the United States and followed Arnim Zola's scheme to become part of SHIELD, which was born out of the Strategic Scientific Reserve (SSR) when the war was over. Zola was still alive in the 1950s - he hadn't yet built the computer system beneath Camp Lehigh in New Jersey that would house his A.I. after his death - while Wilfred Malick became the leader of Hydra in America. It makes sense that after Sousa learned Hydra was still active in the '50s that the insidious terror network adjusted their activities to ensure they wouldn't be discovered by SHIELD again.
Hydra hid within SHIELD so well that the MCU's finest minds of the era, like Peggy Carter, Howard Stark, and Hank Pym, never suspected their enemy was working alongside them all along. Taking out Sousa was, apparently, a key factor in Hydra's success, thanks to the lesson they learned in how to better cover their tracks from SHIELD's top brass noticing their existence. As for how the Chronicoms could further factor into Hydra's infestation of SHIELD and to what extent Coulson and his team affected history, these are questions Agents of SHIELD season 7 will no doubt answer.
