Agents of SHIELD season 7 has officially changed the MCU timeline by moving up a major event decades earlier. The seventh and final season of Marvel's Agents of SHIELD is essentially a joyride through Marvel history. An alien race known as the Chronicoms are attempting to rewrite the past in order to ensure they can conquer Earth in the present. The SHIELD team has cracked time travel as well, and they're desperately attempting to prevent the Chronicoms succeeding.
Agents of SHIELD season 7, episode 5 sees SHIELD arrive in 1973. There, they discover Hydra is working on Project Insight, an orbital satellite that will target every potential threat to their own conquest of Earth. This, of course, was the project from Captain America: The Winter Soldier - which is set in 2014. Hydra's timetable appears to have moved forward 50 years courtesy of the Chronicoms, meaning there is no Captain America to stop them this time. The SHIELD team is understandably shocked at what appears to have been a rewrite of history, but they hope they can still get things on track. After all, the '70s version of Project Insight is based at the Lighthouse, and that facility's existence had been mysteriously erased from SHIELD records in season 5; so it could be the original 1970s Project Insight was simply concealed. The timeline could still work - just about.
A close look at Agents of SHIELD season 7, episode 5 confirms the timeline has been decisively changed. The core problem is Wilfred Malick, who is still alive and working with his son Nathaniel as major figures in Hydra. As confirmed in Agents of SHIELD season 3, Wilfred Malick should have died in 1970; shortly after, Nathaniel was transported to the planet Maveth in an ancient Hydra ritual, his death orchestrated by his brother Gideon Malick. Both Wilfred and Nathaniel are confirmed alive and active on Earth in 1973, and - later in the episode - in 1976. The Chronicoms have clearly created a brand new timeline.
It's difficult to say what the long-term repercussions of this will be, not least because Agents of SHIELD hasn't been especially clear about how its model of time travel works. It's possible the Chronicoms have created a branching timeline in the Multiverse, but in Agents of SHIELD season 7, episode 2 Simmons hinted there is just a single timeline, one future that could potentially be rewritten by altering the past. Whatever the case may be, the future now in the works is a lot more dangerous - and it will be very different to the original timeline. SHIELD destroyed Project Insight in 1976, but Hydra still possess the list of potential threats they intended to be eliminated. It's not hard to imagine them quietly assassinating the young Bruce Banner, for example, who would only be a seven-year-old in 1976. SHIELD has passed the point of no return, and the future is now in motion.
It remains to be seen whether these changes will stand, or whether SHIELD will instead travel back in time and attempt to stop the Chronicoms allying with Hydra back in 1955. They'll need help to do that, given according to Simmons it's only possible to travel backwards in time using the Time Monolith. Fortunately Fitz is still out there, and he does possess a chunk of the Time Monolith, meaning there's still hope for Agents of SHIELD.