The show is naturally stuffed to the brim with references to the rest of the MCU, including:
- The explosions in the first episode (as well as the source of Mike Peterson's powers) are a result of Extremis. Even better, they find this out via recreating the scene of the crime in a massive hologram, outdoing Tony in the movie by making it act like a Pensieve Flashback as well.
- Thor is mentioned by name in a conversation between Agent Ward and Maria Hill.Ward: I don't think Thor's technically a god.
Hill: You haven't seen his arms. - The first time we see Ward, he is recovering a "Chitauri neural link", presumably a relic from the events of The Avengers.
- Coulson cracks a one-liner at Tony Stark's expense.
- Coulson mentions that the last 0-8-4 was a hammer.
- Lola turns out to have tech from the anti-gravity car that Howard Stark invented in the 1940s.
- Ward is stated as having the highest grades as a Stealth Expert for an agent since Romanov.
- Mike notes that it depends on "what kind of person you are" in reference to his powers.
- The first user of the Centipede device acts similarly to Emil Blonsky after his super soldier serum injection in The Incredible Hulk, yelling at the lab worker "I want to feel more!"
- While talking to Ward and May about recruiting Skye as a consultant, Coulson mentions that "technically Stark is one".
- The 0-8-4 from the episode of the same name is HYDRA tech.
- Skye mentions that S.H.I.E.L.D. had covered up New Mexico and Project Pegasus
(where they were studying the Tesseract). - Coulson mentions sacrificing his card collection to help Fury in "The Asset".
- Inverted in the pilot; Ward tells Maria Hill that he is level 6 and knows that Coulson died on the Helicarrier. Coulson emerges from the shadows and says, "Welcome to Level 7." Later, Ward asks if the Avengers know that Coulson is alive. Coulson says they aren't cleared Level 7.
- In "The Asset", Dr. Hall mentions the S.H.I.E.L.D. Tesseract experiments seen in The Avengers.
- In "Girl in the Flower Dress", Coulson uses the same type of bomb used in Iron Man to open the door. He and the team even turns their back to the bomb like in Iron Man.
- Agent Blake, from The Avengers Blu Ray bonus short film "Item 47", appears in "FZZT". ("Item 47" featured criminals who end up being recruited to S.H.I.E.L.D. as technical experts, in the same way Skye joined up. Blake, along with Agent Sitwell, was assigned to recover alien technology that had fallen into civilian hands; very much a proto-Agents of S.H.I.E.L.D. mission.)
- The Chitauri helmet artifact and the virus it carries which Simmons becomes infected with were relics left in the wreckage after the Battle of New York.
- Agent Jasper Sitwell, who appeared with Coulson in "The Consultant" short film, makes an appearance in "The Hub."
- Agents Barton and Romanov (aka Hawkeye and Black Widow) of The Avengers are mentioned in the same episode; apparently they are the only S.H.I.E.L.D. agents who are badass enough to go on missions without an extraction team. Which the movie confirmed in Romanov's case.
- "The Well" picks up directly after the events of Thor: The Dark World, with the team helping on cleanup of the university campus after the battle, and then dealing with some leftover Asgardian business.
- In "The Well", Coulson gives a small reference to his former cellist girlfriend from Portland. She's brought up again in "The Magical Place" as part of Raina's attempt to get Coulson to work with her. She appears in person, played by Amy Acker, in "The Only Light in the Darkness".
- In "The Bridge", Mike mentions having bought his son a complete set of Avengers action figures. In the pilot episode, the boy was shown looking at said toys in a store window, though he claimed he didn't want any due to their shaky financial situation.
- In "The Magical Place", Edison Po is killed using a sonic device like the one Stane used all the way back in the first Iron Man.
- Vanchat is mentioned in "Pilot" as the one selling a Chitauri Neural Link in the black market, most of which is bought by Project Centipede to use in their devices. He's also mentioned in "Eye Spy" as the one responsible for killing a S.H.I.E.L.D. team and keeping Akela Amador prisoner before selling her to Centipede. He finally appears in "The Magical Place", still selling chitauri metal. His capture and interrogation at the hands of Agent Ward leads to S.H.I.E.L.D. raiding Centipede locations all over the world.
- In "Seeds", Bucky Barnes is listed on the S.H.I.E.L.D. memorial at the academy. Also doubles as a bit of foreshadowing for Captain America: The Winter Soldier. In the same episode, Simmons mentions HYDRA from Captain America: The First Avenger and A.I.M. from Iron Man 3 while giving a lecture about the possibility of science being used for nefarious purposes.
- Coulson threatens to have Ward assigned to Blonsky's cell in Alaska if his relationship with May threatens the team.
- Sif from the Thor movies appears in "Yes Men".
- The reason she appears is because an Asgardian criminal escaped during Malekith's Dark Elf Invasion.
- Sif's prior appearance on Earth is how the team identifies her as a friend of Thor and therefore an ally. Coulson later mentions her role in the battle with the Destroyer when vouching for her combat prowess. They also don't know her name, because S.H.I.E.L.D. never learned it in the movie.
- When she first sees Coulson, Sif is initially shocked and suspicious, having heard of his death from Thor.
- She also refers to him the same way Thor did in his first movie, as "Son of Coul".
- In the same episode, Sif mentions the Kree, one of the alien races featured in Guardians of the Galaxy (2014).
- After recapturing Lorelei, Sif mentions that Odin has ordered her brought back to Asgard alive. Audience members who've seen the film will know that Odin has been replaced by Loki in disguise, hence his desire to have a dangerous enemy returned unharmed.
- In "End of the Beginning", Agent Sitwell is told by Agent Hand that he is being reassigned to the Lemurian Star, the S.H.I.E.L.D. freighter he is seen onboard at the beginning of Captain America: The Winter Soldier. All episodes immediately following this one relate directly to the events of Winter Soldier.
- In "Turn, Turn, Turn," Fitz mentions that the "mouse hole" laser cutter that he and the team use to escape the Bus is something he developed but was never mass-distributed. In Captain America: The Winter Soldier, Nick Fury and Maria Hill use the device. Garrett mentions that "the top agents always want the good stuff for themselves."
- Natasha "Black Widow" Romanoff gets a name-check in "Providence", as does Maria Hill. Agent Koenig also says that he's been living at the titular S.H.I.E.L.D. outpost since the Chitauri's invasion of New York.
- "The Only Light in Darkness" contains yet another Shout-Out to Black Widow, as well as a piece of energy absorption technology designed by Bruce Banner. Triplett is also revealed to be the grandson of a Howling Commando from Captain America: The First Avenger.
- The opening scene of "Nothing Personal" shows Maria Hill on the phone to Pepper Potts. Pepper is now Hill's boss at Stark Industries, following her resignation from S.H.I.E.L.D. at the end of Captain America: The Winter Soldier. During their conversation, Hill paraphrases Tony Stark's "privatizing world peace" line from Iron Man 2, which is apparently now something of a company mandate.
- In "Beginning of the End", Nick Fury shows up to give Coulson a weapon to fight the Centipede soldiers: the BFG he used on Loki in The Avengers. He also finally explains why Coulson's death in The Avengers was undone. The episode also directly references his actions following the events of Captain America: The Winter Soldier.
- Coulson: I know what it does.
- In "Face My Enemy," HYDRA is shown in possession of the same type of holographic mask and voice replication technology used by Black Widow in Captain America: The Winter Soldier.
- A Freeze-Frame Bonus shows that Melinda has Black Widow's number in her cellphone.
- In "A Hen in the Wolf House", Whitehall mentions "Our founder" and "his Tesseract".
- Whitehall's statement in the opening of "Shadows":Whitehall: Oh, there's no reason left to fear the Red Skull. He's dead. However, his vision is not. The work HYDRA has done will live on.
- In "The Writing On The Wall", Ward mentions Baron von Strucker, who was last seen experimenting on Wanda and Pietro Maximoff in The Stinger of The Winter Soldier.
- "The Things We Bury" opens with a flashback to 1945, where Whitehall is shown being informed of the Red Skull's death from the end of The First Avenger.
- "Who You Really Are" contains references to Heimdall and his powers, as well as "Odin" ( Loki in disguise) sending Sif to Earth to capture a Kree.
- When he's first seen in "One of Us", Angar the Screamer is shown fitted with the same type of gag used on Loki at the end of The Avengers.
- "The Dirty Half Dozen" ends with Coulson sending Baron Strucker's location to Maria Hill and the Avengers, directly setting up the events of Avengers: Age of Ultron. Meanwhile, Raina experiences a premonition of Loki's scepter and the rise of Ultron.
- In the Season 3 premier, Daisy states that the world has been on edge ever since Ultron attacked Sokovia.
- Coulson states that Fitz briefly thought Simmons may have been shrunken after he heard about the incident at Pym Technologies.
- The news ticker in "Watchdogs" mentions a brutal gang war in Hell's Kitchen.
- A reporter in "Lockup" mentions that Director Mace risked his life to protect people during Helmut Zemo's terrorist attack in Vienna.
- When Mace is shot at in "The Patriot", it fizzles in the podium he blocked it with and then explodes, clearly a Judas bullet from Luke Cage.
- When the team returns from the future in "All the Comforts of Home" Noah gives them a rundown of current events including an Asgardian sighting in New York.
- The flashbacks in "Rise and Shine" Call-Forward to many HYDRA events, as well as one scene set during Captain America: The Winter Soldier.
- "Option Two" mentions "weird stuff happening in New York". (The remainder of the season takes place over a single day, presumably concluding before the film's Cliffhanger.)
