Warning: SPOILERS below for Avengers: Endgame and Marvel's Agents of S.H.I.E.L.D. season 6 premiere.
How does Marvel's Agents of S.H.I.E.L.D. season 6 address the events of Thanos' Decimation snap and Avengers: Endgame? At the conclusion of Agents of S.H.I.E.L.D. season 5, the team led by Phil Coulson fought off an alien invasion by the Confederacy, who were demanding Gravitonium and Inhumans in exchange for protection from Thanos. Key moments in S.H.I.E.L.D. season 5's final episodes even lined up with Avengers: Infinity War's attack of New York by the Black Order in the MCU timeline. However, as every Marvel fan is aware, Thanos won and killed half of all life in the universe with the Infinity Gauntlet.
As fans saw in Avengers: Endgame, for five years, the entire MCU lived with the consequences of the Decimation and the loss of half of all living beings; on Earth, life is somber and tragic as the survivors are forced to adjust to this new reality. The MCU timeline leaps ahead to 2023, which is when the Avengers stage time heists to steal the Infinity Stones from the past and restore the billions of lives lost. By the conclusion of Avengers: Endgame, the MCU movies remain set in 2023 and are poised to move forward from that point. But how does Agents of S.H.I.E.L.D. react to these events?
In short, Agents of S.H.I.E.L.D. doesn't reference Thanos' snap or the events of Avengers: Endgame at all. To add extra confusion for MCU fans, Agents of S.H.I.E.L.D. season 6 is set one year after season 5, which ended with the death of Phil Coulson in Tahiti. In the MCU timeline, this technically means that Agents of S.H.I.E.L.D. season 6 should be happening roughly one year after the Decimation, yet the series doesn't reflect the grim reality depicted in Avengers: Endgame where half of humanity is missing. There's also no reference made to Thanos or the Decimation, whether the Agents are in outer space or back on Earth.
Instead, Agents of S.H.I.E.L.D. splits its action between Earth and outer space. One team, comprised of Daisy Johnson, Jemma Simmons, and Agents Davis and Piper are searching for the missing Leo Fitz, who is supposed to still be cryogenically frozen in order to reunite with his team in the Lighthouse almost 90 years in the future.
Meanwhile back on Earth, S.H.I.E.L.D.'s new director Alphonso "Mack" Mackenzie, Melinda May, and Yo-Yo Rodriguez are tracking incursions into their reality occurring via portals found along ley lines and they encounter Sarge, a mysterious doppelganger of the late Phil Coulson. Unfortunately, the strange portals don't resemble the magical circles Doctor Strange and Wong used in Avengers: Endgame, so Agents of S.H.I.E.L.D. missed the chance to even have that tiny connection with the film.
While it's frustrating to see no correlation between Agents of S.H.I.E.L.D. and Avengers: Endgame, especially since the ABC series is supposed to tie into the MCU movies, one possible explanation is that S.H.I.E.L.D.'s use of time travel in season 5 could have created its own separate timeline branch. The Ancient One and Professor Hulk offered some explanation for how new, branching timelines work in Avengers: Endgame and there's a chance that Agents of S.H.I.E.L.D. season 5 created its own reality separate from the MCU movies, as evidenced by how the Earth was destroyed 90 years in the future, something the MCU movies have not acknowledged (and likely never will). However, it's also possible Agents of S.H.I.E.L.D. is now happening as one of the 14,000,605 futures Doctor Strange saw.
Considering how none of the Agents, not even the superpowered Quake, were invited to the final battle against Thanos in Avengers: Endgame, it appears that Agents of S.H.I.E.L.D. may no longer be connected to the MCU movies and is making up its own rules from here on in, which is probably for the best.
Marvel's Agents of S.H.I.E.L.D. season 6 airs Fridays @ 8pm on ABC.