While S.H.I.E.L.D. was virtually absent from Iron Man 3 and Thor: The Dark World, the organization took center stage in Captain America: The Winter Solider -- and not in a good way. The Winter Soldier unearthed the fact that Hydra was not only alive and well, but deeply embedded in S.H.I.E.L.D. As Arnim Zola revealed to Rodgers and Romanoff, Hydra scientists were recruited to S.H.I.E.L.D. as a part of Project Paperclip. Zola helped Hydra grow "like a beautiful parasite" within S.H.I.E.L.D. Under S.H.I.E.L.D.'s nose, Hydra incited crises and encouraged wars, aiming to cause enough chaos that humanity would willingly surrender to a new world order.
In order to end Hydra, Captain America also had to destroy S.H.I.E.L.D. Though he successfully stopped Hydra and Project Insight, S.H.I.E.L.D. still had to reckon with the damage it caused over the decades. As unwitting as it may have been, S.H.I.E.L.D. allowed Hydra to operate for years; worse, this may not have been a problem if Project Paperclip had never been enacted. As such, S.H.I.E.L.D. was dissolved.
Ant-Man also revealed another side of S.H.I.E.L.D. In a flashback to 1989, Hank Pym confronted S.H.I.E.L.D. leaders like Peggy Carter, Howard Stark and Mitchell Carson. Carson, of course, was later revealed as a Hydra agent in the film. Prior to that, though, he attempted to steal the Pym particle formula. While Carter and Stark seemed surprised at the news, Stark didn't seem to disagree with the idea that the formula should be accessible to S.H.I.E.L.D. Both circumstances prompted Pym to quit S.H.I.E.L.D. in a rage, despite his years of work for them and the sacrifices he made on his missions.
Although S.H.I.E.L.D. disbanded in The Winter Soldier, pieces of it lived on. For instance, Fury had a spare helicarrier in case of emergency and used it to save the day in Avengers: Age of Ultron; this may even be one of S.H.I.E.L.D.'s finer moments, as it only stepped in to save civilians, not participate in the battle against Ultron. Sharon Carter -- who joined the C.I.A. after S.H.I.E.L.D.'s fall -- also turned up in Captain America: Civil War to help Steve find Bucky. In this capacity, S.H.I.E.L.D. was infinitely more helpful than when it was an official organization.
Finally, Ant-Man and the Wasp showed two very different aspects of S.H.I.E.L.D. For one, it introduced Jimmy Woo, who is a key member of S.H.I.E.L.D. in the comics. In the movie, though, Woo -- now an F.B.I. agent -- was a bit more bumbling and provided comic relief rather than support for Scott Lang. Despite some valiant efforts, Woo just never could catch Scott in the act of violating the terms of his home arrest. Nevertheless, Woo's dedication to his job provided some serious obstacles for Scott, Pym and Hope van Dyne as they desperately tried to free Janet van Dyne from the Quantum Zone. Despite his good intentions, he is positioned as an antagonist, only by virtue of the fact that he had good reason to believe Scott was breaking the law.
On the flip side, Ghost is a direct product of S.H.I.E.L.D.'s actions. Her powers are a result of her father Elihas Starr's attempts to recreate Pym's experiments. Though he died in the resulting explosion, she was given the power to phase through solid objects. However, the process of ripping her molecules apart and stitching them back together caused her great pain and would eventually lead to her death unless a cure was found. Bill Foster promised to heal her and did his best to do so, but to no avail. In the meantime, S.H.I.E.L.D. found a use for her. The organization trained her as an assassin, wielding her painful powers as a weapon. In other words, S.H.I.E.L.D. took advantage of her condition and never found a cure for her before its collapse.
Overall, S.H.I.E.L.D. may have done a bit more harm than good, at least so far as the MCU's films are concerned. In fact, the organization has played an almost antagonistic role in several of the MCU's 20 films. Hopefully, S.H.I.E.L.D. will get shown in a better light during the events of Captain Marvel, which takes place in the 90s and stars characters like Phil Coulson and Nick Fury. As it stands, though, S.H.I.E.L.D. has a lot to atone for.
In theaters now, Ant-Man and The Wasp stars Paul Rudd, Evangeline Lilly, Bobby Cannavale, Michael Peña, Tip “T.I.” Harris, Judy Greer, David Dastmalchian, Michael Douglas, Michelle Pfeiffer, Laurence Fishburne, Hannah John-Kamen, Randall Park and Walton Goggins.