How Will 'Captain America: The Winter Soldier' Affect 'Agents of S.H.I.E.L.D.'? Short Answer: Heavily
With the release of Captain America: The Winter Soldier on April 4, Marvel took its cohesive Avengers universe to the next step, creating even more complex connections between its movies and sole TV series. All season, Agents of S.H.I.E.L.D. has proved that it fits within that cinematic universe, bringing on Nick Fury and Thor's Sif and referencing plot points from various films. However with its newest film, things just got very, very complicated, as the end of The Winter Soldier has a huge effect on SHIELD . (Winter Soldier and SHIELD spoilers ahead.)
It's been made very clear that the two will be very closely connected and the April 1 episode of SHIELD contained a few themes and small details that directly influenced The Winter Soldier. In "End of the Beginning" Agent Sitwell leaves Coulson's bus because he's called to a mission on a boat. In The Winter Soldier, Captain America is sent to rescue Sitwell and a group of hostages from a pirated boat.
"End of the Beginning" also confirms that Coulson was right to be suspicious of SHIELD, as Victoria Hand is up to something and wants his whole team killed. Then Winter Soldier shows that the corruption within the organization goes way above Hand, and that the sinister HYDRA has secretly been operating within it for decades. Up to this point, the connections between the movie and the show worked well. You didn't need to watch SHIELD to understand The Winter Soldier, but if you did, you were rewarded with some references and thematic continuity. However, The Winter Soldier's intense ending has ramifications that will be felt in every future Avengers film, and need to be addressed on SHEILD in a major way.
Because of HYDRA's involvement, Captain America, Nick Fury, Maria Hill, Falcon and Black Widow decided to not just destroy S.H.I.E.L.D.'s dangerous new weapons, but the agency itself. At the film's end, each of the heroes is on their own mission, and other innocent agent have moved on to work for other government agencies, or in the case of Hill, Stark Industries.
As the title shows, S.H.I.E.L.D. is a pretty important part of SHIELD, considering its predicated on special group of agents and one of the most recent mysteries has centered on what exactly happened to Coulson when he was brought back to life—on Fury's orders. Fury's gone to spy in Europe and while Coulson's team using a plane as headquarters means they weren't involved in the destruction of S.H.I.E.L.D. headquarters, they no longer have an agency to belong to. The title of the series itself becomes meaningless. What the hell is ABC gonna do?
It's risky either way. SHIELD's cast and producers have said that The Winter Soldier will greatly affect the show, but not exactly how. If the next episode, "Turn, Turn, Turn," brings up too much from The Winter Soldier, fans who haven't seen it will be confused and pretty annoyed. If it ignore the film's events, the whole Marvel Universe will be disrupted, and viewers who have seen the film will be confused. According to SHIELD'S executive producer Maurissa Tancharoen, she and Joss Whedon have known what was coming in The Winter Soldier all along. But that doesn't mean they're going to handle it well.
Tying together so many movies must be difficult enough, adding a TV show whose ratings don't remotely compare to the monstrous success of those movies just complicates things even further. It's not even about pleasing everyone, it's about maintaining a cinematic universe that took years to build. One misstep and a single episode of television brings it all down.
So no pressure, SHIELD, it's only the fate of a multi-billion dollar universe hanging in the balance.