There's simply no way to make Marvel's Agents of SHIELD season 6 fit with the MCU timeline. When Marvel Television launched Agents of SHIELD back in 2013, they envisioned the show as having the closest possible connections to the movies themselves. The first season kicked off with explicit references to events in the recently-released Iron Man 3, had a dedicated tie-in episode to Thor: The Dark World, and ultimately reoriented its entire plot around the fall of SHIELD in Captain America: The Winter Soldier. That pattern continued through season 2, with an arc that tied into Avengers: Age of Ultron.
Everything changed in 2015, when behind-the-scenes conflict at Marvel led Disney to force a corporate restructure. Marvel Studios was pulled out of the wider Marvel Entertainment group, and established as a separate Disney subsidiary. From that point on, the links between Marvel Studios and Marvel Television became noticeably more distant, and - with the exception of a throwaway reference to Pym Particles at the beginning of Agents of SHIELD season 3 - connections became thematic rather than explicit. And yet, Marvel Television was careful to stress the continuing passage of time, with explicit six-month gaps between most seasons.
The time travel plot in Agents of SHIELD season 5 appeared to offer the show a chance to do something of a reset. The bulk of the team was transported to a dystopian future where the Earth had been shattered like an egg, and Fitz soon joined them by going the long way round, via cryogenic suspension. When they eventually returned to the present, Agents of SHIELD could have broken away from the main MCU timeline and ran behind the movies for a while to avoid any complications with universe-changing events. But it wasn't the approach Marvel Television chose to take.
How Agents of SHIELD Season 5 Tied Into Avengers: Infinity War
Back in 2017, Marvel Studios was building up to the biggest event in the history of the MCU, the culmination of a decade's worth of serialized storytelling on the big screen. And the showrunners of Agents of SHIELD decided they definitely wanted to tie into that for what they believed would be their final season.
When the SHIELD team finally returned home in season 5, episode 11, they found themselves in a new base of operations, the Lighthouse. This had been used by the Chronicom anthropologists Enoch and Noah to monitor the Earth for potential threats; while SHIELD were still settling in, getting used to their new surroundings, they detected "two Asgardians in the city." It was a clear nod to Thor: Ragnarok, where Thor and Loki briefly visited New York. Viewers immediately knew that Agents of SHIELD was joining the countdown to Avengers: Infinity War and the arrival of Thanos.
SHIELD soon found themselves navigating a conspiracy between the last vestiges of Hydra and an alien Confederacy. In a surprise twist, it turned out the Confederacy had manipulated Hydra by offering knowledge of Thanos and his armies, who they insisted would return to Earth after their defeat in 2012. Later episodes featured dialogue confirming that it was concurrent to the beginning of Avengers: Infinity War, with Thanos' forces launching their initial attack on New York in order to acquire the Time Stone. In a strange sense, Thanos himself was the villain of Agents of SHIELD season 5.
But then, incredibly, the Agents of SHIELD season 5 finale ignored the moment Thanos snapped his fingers and erased half the life in the universe. The biggest single event in the history of the MCU was sidestepped by the official tie-in TV series. From a production standpoint, it made sense; the writers and showrunners believed season 5 was the end of the road for Agents of SHIELD (they even called the season 5 finale "The End"). They wanted to tie up all the loose ends, resolve the main character arcs, and finish on an optimistic note. All that would have been completely overshadowed by the snap.
There was just one problem with this approach: ABC surprised Marvel by renewing Agents of SHIELD for a sixth season.
Agents of SHIELD Season 6 Continued To Ignore Infinity War
Agents of SHIELD season 6 is explicitly set one year after the events of the season 5 finale; Mack has had a year to rebuild SHIELD, while Quake and Simmons have been in space looking for Fitz for the past twelve months. Agents of SHIELD season 6, episode 9 further cemented the timeline in a scene where Mack reminisced with Daisy, remembering all the weird stuff they've dealt with together over the course of the last five years. Mack joined up with SHIELD in 2014, after the Hydra uprising in Captain America: The Winter Soldier, which confirms that season 6 is set in 2019. That's a full year after Thanos snapped his fingers.
For all this is the case, Agents of SHIELD season 6 is clearly set in a world in which the snap never happened, an Earth just like ours but with superheroes. There's no hint that civilization has been almost brought down by the sudden disappearance of half the life on Earth, and there isn't a trace of the kind of PTSD and trauma shown in Avengers: Endgame. The problem isn't restricted to Earth, either; a good chunk of season 6 is based in space, and yet none of the alien civilizations visited by Quake and Simmons have been affected by any cosmic trauma either. According to Avengers: Endgame, when Thanos snapped his fingers Earth became ground zero for a wave of cosmic energy of unparalleled magnitude. You'd have expected a lot of alien races to have checked Earth out after the snap, but in Agents of SHIELD, Terrans are only known because of the actions of Quake and her team.
Again, there's a simple reason for this: Marvel Television had no idea what Marvel Studios' plans were. "Just looking at it from a very practical place," Marvel TV head Jeph Loeb explained, "which is, what the world looked like post-snap, [it] was not something we had seen yet. We were already shooting." As a result, Loeb suggested that every Marvel Television show is to be considered set pre-snap - including Agents of SHIELD season 6. That would essentially mean that Thanos' snap hasn't been ignored; it just hasn't happened yet. The one problem with this argument, however, is that it flatly contradicts the events of the show itself. Agents of SHIELD season 5 was explicitly concurrent to Avenger: Infinity War, and season 6 is set one year later, in 2019. There's no easy way to reconcile this.
Agents of SHIELD Can't Fit The MCU (& That's OK)
The truth is that Marvel Television and Marvel Studios have grown apart over the last few years. The corporate restructure back in 2015 inevitably meant that, sooner or later, the prime canon of the movies was going to do something the TV side just couldn't accommodate without it taking over every single one of their shows. That hasn't been too big a problem for the likes of Cloak & Dagger and Runaways, which have carefully avoided giving any specific sense of where they fit into the timeline, but Agents of SHIELD was always going to take the hit.
Ultimately, the real question is whether or not it matters anymore. Agents of SHIELD has effectively outgrown the MCU, and has developed a mythology of its own, one that's every bit as rich as Marvel Studios'. Nowadays, this is a show that explores Framework virtual realities and LMDs, Monoliths and jump drives, rather than the latest concepts developed on the big screen.
And this is only going to continue as Agents of SHIELD moves towards its end. Marvel TV head Jeph Loeb has openly stated that he has no idea when ABC will choose to air season 7 next year, which means there won't even be any tie-ins to The Eternals and Black Widow - otherwise the release would be carefully coordinated. While it's conceivable that season 7's time travel could find a fix to Agents of SHIELD's continuity by rewriting history somehow, it doesn't really need to. And, frankly, the writers would be better served ignoring the issue and just ensuring their show bows out in style.
More: Theory: Agents Of SHIELD Is Now In An Alternate MCU Timeline