WARNING: The following article contains spoilers for Captain Marvel, in theaters now.
Set primarily in 1995, Captain Marvel explores a previously unseen period within the Marvel Cinematic Universe, detailing the early days of Nick Fury and Phil Coulson with S.H.I.E.L.D. in a world that hasn't experienced active superheroes since the original Ant-Man and The Wasp during the Cold War.
As such, there are revelations in the film that subvert our notions of the MCU while filling in the chronological gaps within its history. The following are some of the biggest changes to familiar locations, expectations and characters, as depicted in Captain Marvel.
First seen in the post-credits of 2011's Thor, Project P.E.G.A.S.U.S. is a remote S.H.I.E.L.D. and NASA facility in which the Tesseract is eventually kept and experimented on before the building's destruction at the hands of Loki in The Avengers.
Captain Marvel reveals that, before obtaining the Space Stone, the facility is used as a hangar to house experimental aircraft, and an archives for top-secret military records where Carol Danvers will discover her true past on Earth.
Ever since fans learned that Skrulls would make their MCU debut in the film, it was widely speculated this would set up an adaptation of the Marvel Comics storyline Secret Invasion. This assumption was later supported by trailers and promotional materials depicting the shape-shifting aliens infiltrating S.H.I.E.L.D. to further an unspecified agenda.
Over the course of Captain Marvel, it's revealed the Skrulls are actually refugees, fighting a losing war against the militaristic Kree. While they do, in fact, infiltrate S.H.I.E.L.D. to a degree and nearly kill Nick Fury on multiple occasions, they ultimately abandon any pretenses of conquering Earth, and instead depart with Carol Danvers to find a new home world on the other side of the universe.
The main mode of transportation for the Avengers after making its MCU debut in the 2012 ensemble film, the Quinjet is capable of venturing into deep space as the means the Hulk used to arrive on Sakaar sometime before the events of Thor: Ragnarok.
The aircraft's predecessor, the Quadjet, is introduced in Captain Marvel as a more compact vehicle, appropriately fitted with four engines instead of its successor's five. Initially incapable of leaving Earth's atmosphere, modifications by the Skrulls allow the Quadjet to enter the planet's orbit, likely improved upon by S.H.I.E.L.D. when designing the subsequent Quinjet.
Much of Phase One of the MCU revolved around the Tesseract, later revealed to be the vessel for the Space Stone. Recovered by the Red Skull in Norway during World War II to power Hydra's war machine, the cosmic cube was recovered by Howard Stark at the end of Captain America: The First Avenger and seen in S.H.I.E.L.D. custody by the conclusion of Thor. Thanos taked Loki with recovering the cube in The Avengers before Thor brought it back to Asgard for its temporary safekeeping.
The Infinity Stone is revealed to play a vital role in Carol Danvers' transformation as the centerpiece of Mar-Vell's experiments to create a lights-peed engine. After Yon-Rogg attacks and kills Mar-Vell and attempts to recover the cube for himself, Carol destroys the engine, inadvertently bombarding herself with its energy to gain superpowers. The Tesseract is stored on Mar-Vell's secret lab orbiting Earth before being temporarily eaten by the alien feline Goose. In the post-credits scene to the film, Goose is seen vomiting the fully intact Tesseract on to Nick Fury's desk, revealing how it came into S.H.I.E.L.D. custody. How Mar-Vell recovered the cube from Howard Stark remains a mystery.
The greatest spy in the MCU, Nick Fury was the early link to the individual films, from 2008's Iron Man through The Avengers. As the director of S.H.I.E.L.D., Fury is responsible for forming the Avengers while safeguarding the world from all manner of extraordinary threats. He has always been seen sporting an eye patch to cover a lost left eye, which he attributes in Captain America: The Winter Soldier to an unexpected betrayal.
Captain Marvel provides the most extensive look at Fury's backstory yet, with the up-and-coming S.H.I.E.L.D. operative explaining his life in Alabama and his previous military service before going into the top-secret intelligence community. While retconning that the acronym was in wider usage before Coulson branded it at the end of Iron Man, Captain Marvel hints that Fury is fast-tracked for promotion due to his role in the film rather than rescuing Alexander Pierce in Colombia as mentioned in The Winter Soldier. And the loss of his eye is revealed not to be due to a covert betrayal but rather from the claws of the Flerkin, Goose.
The long-term plan of Fury to unite the Earth's heroes to protect it against threats far beyond conventional military defenses, the Avenger Initiative is cited by the S.H.I.E.L.D. director in his very first appearance in the post-credits scene for Iron Man. Years later, Tony Stark reviews files from the initiative, providing backgrounds on the Hulk, Thor and Captain America.
The final scene of Captain Marvel shows Fury back in his office after his out-of-this-world adventure. Recuperating from the recent loss of his eye, Fury tasks Coulson with locating more extraordinary individuals as he types his plans for the Avengers inspired by his mission with Captain Marvel. Originally titled "The Protector Initiative," Fury notices Carol Danvers' Air Force call sign was "Avenger" and renames his plans accordingly.
Directed by Anna Boden and Ryan Fleck, Captain Marvel stars Brie Larson as Carol Danvers, Samuel L. Jackson as Nick Fury, Jude Law as the commander of Starforce, Clark Gregg as Phil Coulson, Lee Pace as Ronan the Accuser, Djimon Hounsou as Korath the Pursuer, Gemma Chan as Minn-Erva, Ben Mendelsohn as Talos, Lashana Lynch as Maria Rambeau, Algenis Perez Soto as Att-Lass, McKenna Grace as a young Carol Danvers and Annette Bening as the Supreme Intelligence.