The popularity of the Marvel Cinematic Universe has had resonant effects on Marvel Comics proper. With Marvel understandably wanting fans of the films to be able to find something in the comics that would appeal to them, aspects of the Marvel Universe morphed to better line up with the MCU.
This phenomenon is no more pronounced than the changes made to S.H.I.E.L.D. in Marvel Comics after the popularity of the MCU films. However, whereas changes made to Hawkeye, Captain America, and others are largely aesthetic, the changes to S.H.I.E.L.D. are more in-depth and have altered the destiny of the global intelligence and defense organization that we all know and love.
10 Introducing Agent Phil Coulson
The first and most prominent change to S.H.I.E.L.D. in Marvel Comics was the introduction of beloved S.H.I.E.L.D. agent and early connection between the movies in the MCU, Agent Phil Coulson. He first appeared in the Battle Scars comic, initially as "Cheese" and later by Phil Coulson.
He stuck around as an agent of S.H.I.E.L.D. for a long time until he was killed by Deadpool during Secret Empire while trying to interfere in the Hydra Supreme Commander's plans to take over. However, he has since come back to plague the Avengers with his new Squadron Supreme of America as an agent of Mephisto.
9 And Company
This later brought in the cast of the Agents of S.H.I.E.L.D. television series, including Leo Fitz, Jemma Simmons, Melinda May, and Grant Ward.
All characters got funneled into S.H.I.E.L.D. in the comics to add their on-screen charms to the pages of the Marvel Comics Universe.
8 Resurgence Of Mockingbird
Avenger and S.H.I.E.L.D. agent Bobbi Morse, aka Mockingbird, got something of a resurgence in the comics thanks to her appearance in the Agents of S.H.I.E.L.D television series, as played by Adrianne Palicki. She received her own excellent yet short-lived solo series by Chelsea Cain and Kate Niemczyk. It also brought back the character, Lancelot "Lance" Hunter.
He was a former lover of Bobbi's in the television series despite having never met her in the comics before. Their old relationship in the show brought Hunter back to the comics as an old flame for Bobbi.
7 A New Deathlok
The Agents of S.H.I.E.L.D. television series also gave a shot of life to the less-popular character of Deathlok. While Deathlok had often been native to alternate futures of the Marvel Universe, Henry Hayes became the next Earth-616 Deathlok (formerly Michael Collins).
Michael Peterson was the Deathlok in the TV series, but he doesn't have a perfect analog in Marvel Comics. Henry Hayes would be the closest, but they still have their differences.
6 Agent Daisy Johnson
Skye/Daisy Johnson is one of the most iconic characters from the MCU Agents of S.H.I.E.L.D. TV series, and she did have her origins in Marvel Comics. She first appeared during Nick Fury's Secret War in Latveria. She became part of S.H.I.E.L.D. shortly afterward, but she was recruited into Nick Fury's Secret Warriors to help wage his shadow war against the Skrulls and Hydra.
She was later made director of S.H.I.E.L.D. by Steve Rogers and even became part of his Avengers team. Shortly after the takeoff of the MCU and around the start of Agents of S.H.I.E.L.D., she became another regular Agent of S.H.I.E.L.D. and was even made part of Coulson and Maria Hill's Secret Avengers team.
5 Agent Invisible Woman
The Fantastic Four fell off from Marvel's priority once the MCU took off, as Fox Studios still had the rights to the FF films and had one on the horizon. As such, Marvel temporarily retired the Fantastic Four and began trying to find new places for its members.
Among them was placing Invisible Woman in S.H.I.E.L.D. It was revealed that she had a long history with the organization, and she became an active member yet again.
4 Erik Selvig
Erik Selvig, a part of the supporting cast of the first two Thor films was also brought into S.H.I.EL.D. in Marvel Comics until far later than the Agents of S.H.I.E.L.D. cast.
He was brought in as part of the Pleasant Hill prison operation and became a Hydra defector who partly worked with the corrupted Captain America in the Steve Rogers: Captain America title. He would later kill himself after he and Zemo effectively "killed" the sentient Cosmic Cube, Kobik.
3 The New Nick Fury
Samuel L. Jackson's film rendition of Nick Fury in the MCU is largely based upon the Ultimate Marvel Comics version of the character. As such, it didn't line up with the regular Earth-616 version of Nick Fury. The aforementioned Battle Scars story also introduced Marcus Johnson, aka Nicholas Fury Jr.
He is the son of the Nick Fury that longtime readers had known from Marvel Comics, and he became the new centerpiece of S.H.I.E.L.D. and its associate operations. Meanwhile, Nick Fury Sr. assassinated Uatu the Watcher and was punished by being made into "the Unseen." He was made the immortal replacement for Uatu that could physically never interfere in anything on Earth and beyond.
2 Agents Of S.H.I.E.L.D. Comic
Agents of S.H.I.E.L.D. even got its own comic in the Marvel Comics Universe. It starred the cast from the show in all-new tales that took place in the Marvel Universe we all know and loved.
1 The Fall Of S.H.I.E.L.D.
While the Hydra infiltration of S.H.I.E.L.D. from Captain America: The Winter Soldier seemed to be inspired by the same infiltration spotlighted in the Secret Warriors title, the subsequent fall of S.H.I.E.L.D. was co-opted back into Marvel Comics after the Secret Empire story.
Like the film, Hydra took over the United States government, and it being ousted also spelled the end of S.H.I.E.L.D. as we know it. It's still dissolved in the comics to this day.