Marvel's What If…? Episode 3 dealt with one of the most somber stories since Avengers: Infinity War and Avengers: Endgame. The episode can be explained with one sentence,
"What If... The World Lost its Mightiest Heroes?"
While the third episode of What If...? does not do much to set up the future of the series, it does include a few Easter eggs and callbacks to the movies of MCU Phase 1. The latest episode also explores what would happen if Loki had become the crown prince of Asgard during the events of Thor (2011).
The episode plays out as a classic "Whodunit" murder-mystery as an unidentified serial killer targets potential candidates for the Avengers Initiative.
List of Easter eggs and theories from Episode 2 of Marvel's What If…?
Fury's big week
What If…? Episode 3 gives an alternate reality version of 2012's prelude comic series to the Avengers movie. The comic series titled Fury's Big Week, just like Episode 3, established that the events of Iron Man 2 (2010), The Incredible Hulk (2008), and Thor (2011) happened within a span of a week.
The episode also establishes that Natasha Romanoff went to Betty Ross at Culver University with the injector that seemingly killed Stark. In the original MCU Phase 1 timeline, according to the prelude comic, Natasha went to Culver University to monitor Bruce Banner on Fury's orders.
In the comics, Natasha was also present during the Harlem duel between Hulk and the Abomination.
What If...? episode 3 showcases Fury's experience from Monday to Friday.
Monday - Tony Stark is killed, for which Black Widow gets framed.
Tuesday - Thor Odinson is killed, and Hawkeye is framed for it. Later on, Clint Barton (aka Hawkeye) is also murdered.
Wednesday - Bruce Banner/ the Hulk is killed. Furthermore, Loki comes to Earth (Midgard). Later on, Natasha is killed by the mysterious killer (Hank Pym) after learning his identity.
Thursday - Fury enlists Loki's help to stop Hank Pym.
Friday - Loki takes over Earth as its new ruler.
Fury was later seen going to the Arctic, where Captain America (Steve Rogers) was buried. In this alternate reality, the return of Captain Marvel (Carol Danvers) and the discovery of Steve Rogers in cryostasis occur earlier than in the original MCU timeline.
Hydra reunion
When SHIELD suspects Romanoff of killing Tony Stark, audiences see Crossbones/Brock Rumlow and Jack Rollins earlier. Frank Grillo and Callan Mulvey return to voice their respective characters.
Even SHIELD director and Hydra sleeper agent (like Rumlow and Rollins) Alexander Pierce was referenced in the scene.
Civil War II reference
The third episode of Marvel's What If…? Includes Hawkeye getting framed for Thor's murder. This is similar to 2016's Civil War II Comics Issue #3, where Hawkeye (Clint Barton) is killing Bruce Banner/Hulk.
Coulson's password
While this callback to The Avengers (2012) was not lost on any viewer, Coulson's password regarding Captain America also included Steve's birthday, July 4th.
Winter Soldier murders Hope Van Dyne (Hope Pym)?
In 2014's Captain America: The Winter Soldier, Natasha mentions that Winter Soldier (Bucky Barnes) attacked her near Odessa, Ukraine, and kills the engineer she was supposed to protect.
In What If...? Episode 3, Fury also mentions that Hope was killed on a mission in Odessa. This likely means that Hope was the SHIELD agent who went on the Ukraine mission instead of Romanoff in this reality.
Visual parallels to previous MCU moments
Other than these references, What If...? episode 3 also contained several visual parallels to specific moments in the MCU.