Warning: SPOILERS for Agents of SHIELD's series finale.
The distanced itself from the MCU movies, establishing its own unique lore.
Agents of SHIELD season 7 is the end of the road for Coulson and his team - and it's been a wild ride. This season has seen SHIELD caught up in a sort of Time War against an alien race called the Chronicoms, who were attempting to create a timeline vulnerable to their conquest. SHIELD was tasked with preserving the timeline, but it soon became clear they had apparently failed in this mission. The stakes had never been higher for the SHIELD team, but they also remained disturbingly personal; the Chronicoms altered Mack's personal timeline by killing his parents in the 1980s, while Daisy watched her mother die before she had even been born.
Fortunately, it turned out the Chronicoms had badly underestimated one key member of the SHIELD team, who had been absent from the series until the finale. They hadn't counted on Fitz, who had cracked time travel and orchestrated a desperate plan to stop them.
Agents of SHIELD's Time Travel Explained Properly
Time travel is one of the most difficult concepts in any science-fiction franchise, largely because it has absolutely no real-world analogue. As a result, every franchise tends to establish its own rules, and they're rarely handled in a consistent manner. Agents of SHIELD season 5 had committed to the Multiverse model, with the idea branching timelines could be created as a result of time travel, but it was unclear how easy these branches were to create. In Agents of SHIELD season 7, episode 1, Deke suggested he bought into the timestream theory. "Personally, I subscribe to the timestream idea," he explained. "Imagine time is a stream, right, and we were sticks that were thrown into it."
The stream isn't impeded by one or too many sticks, but if too many are added, it creates a dam that changes the direction of the water. "So, as long as we can avoid that," Deke concluded, "we should be able to splash around a little bit and we're all good." This was the running theory through most of the season, but attentive viewers began to notice weird contradictions. It turns out Deke was completely wrong; the very act of traveling into the past created a brand new timeline, and the divergences increased as the season went on.
Where Fitz Was & Agents of SHIELD's Real Mission
Fitz and Simmons were rescued from the Chronicoms at the tail end of Agents of SHIELD season 6, and it seems they stole an important piece of Chronicom technology that allowed them to view the timelines and even predict what people would do. Using this, Fitz learned there was only one way to save the day - but it involved Avengers: Endgame's own time travel.
Deke's Sacrifice & SHIELD Future Explained
The SHIELD team insisted they couldn't simply leave this new timeline to be conquered by the Chronicoms; it was a real world, after all, not just a virtual Framework, and they felt responsible for it. Fitz came up with a solution; they would jump back to their own timeline through the Quantum Realm, but they would take the Chronicom ships with them, towing them along. It was a smart strategy, but the technology required one member of the team to stay behind.
Sousa initially volunteered, but Deke wouldn't allow that to happen, because he felt Sousa could make Daisy happy. Besides, he reasoned, he'd spent years in 1986 and had built a life for himself as a rock-'n'-roll legend. So Deke was left in the new timeline, one where the SHIELD of 1986 had been decimated, and to his surprise and delight the survivors asked him to take over as director. It's only a shame the Agents of SHIELD season 7 finale is the end of this story, because it would be great to see what Deke made of his own version of SHIELD. What's interesting is that Deke found himself staying in a timeline that was created, which is fitting since he was a remnant of a timeline that no longer exists.
Enoch Was The Key To The Chronicoms' Defeat
Oddly enough, the Agents of SHIELD season 7 finale suggests Enoch - the Chronicom traitor who had sacrificed himself in Agents of SHIELD season 7 - was the key to the Chronicoms' defeat. Enoch's example proved a Chronicom could learn empathy, and that an empathic Chronicom would be an ally rather than an enemy. Fitz's plan was to combine May's new empathic abilities with Kora's - to transmit empathic knowledge to the Chronicoms on Earth, and thus render them harmless. The SHIELD team stole aboard the Chronicom ships, and tricked Sybil into commanding an all-out attack on the Lighthouse. With the Chronicom ground forces concentrated, they only had a single target to hit in order to achieve their goal.
Quake and Nathaniel Battled It Out
But there was a dangerous loose cannon in play; Nathaniel Malick. In the original timeline, Nathaniel Malick had been transported to the planet Maveth as a sacrifice to the Hydra god Hive in 1970. In the new timeline, Nathaniel lived on and became fascinated with the Inhumans, learning the secret of duplicating an Inhuman's powers. He had successfully stolen Quake's abilities, and had added Kora's into the mix as well. SHIELD knew he'd cause trouble, and so they sent Quake to keep Nathaniel busy on the Chronicom flagship while they dealt with the Chronicoms. The Quake-on-Quake fight culminated in a spectacular release of energy near the Chronicom ship's reactors, with the resulting explosion destroying the entire fleet. SHIELD then picked up the dying Quake from space, and Kora used her powers to revive her sister.
Fitz & Simmons' Secret Daughter
With the battle finally over, Fitz and Simmons' greatest secret was finally revealed - and the real reason the team could never come together again. It seems Fitz and Simmons had spent years of their own lives cracking time travel and working out how to stop the Chronicoms. They had done so aboard the Zephyr, hiding in a distant triple-star system Simmons had always loved looking up at as a child.
During those years, their lives had taken a twist when they realized Simmons was unexpectedly pregnant. So they had brought up their daughter, Ayla, aboard the Zephyr. Finally, after several years, they decided it was time to put matters right and save the day; after all, they wanted to give Alya more than just the Zephyr to live on. This was why Simmons had previously grown so distraught when she briefly regained her memories in Agents of SHIELD season 7, episode 9; she had wiped her memory of her daughter in order to protect her, but what mother can possibly stand realizing she has forgotten her own child?
With the Chronicoms defeated, Fitz and Simmons knew they must retire from SHIELD in order to enjoy being parents. There's a curious and emotional inversion between Fitz's story and that of Tony Stark's in Avengers: Endgame. Both scientists cracked time travel, but unlike Stark, Fitz got to live on and have his Happily Ever After with his beloved Simmons and their daughter. A huge part of that, of course, is because Fitz stayed behind instead of leading an all-out war, but the parallel is still there.
Mack Becomes Marvel's New Nick Fury
The Agents of SHIELD season 7 finale fast-forwarded a year, revealing what had happened to the old SHIELD team now they had split up. Mack had remained director of SHIELD, and he'd essentially become the new Nick Fury, even sporting the traditional Fury trench-coat. Mack had clearly rebuilt SHIELD into a powerful, global force for good, and was shown standing on the deck of one of the SHIELD Helicarriers as they prepared to perform a mission. He's certain to be a very different director to Nick Fury, however; less secretive, more consultative, preferring to give his senior staff a lot more leeway.
Yo-Yo's New Team & DC's Flash Reference
Yo-Yo's powers had radically expanded in Agents of SHIELD season 7. She's previously only possessed a limited version of super-speed, with her power manifesting in "bursts" that last as long as a heartbeat; she would always snap back to her point of origin like a yo-yo. But she learned this limitation was actually self-imposed, due to psychological scars she had suffered before even gaining her abilities. With that dealt with, Yo-Yo gained true super-speed, with no restrictions. And, according to the one year later scenes, she'll continue to use her super-speed as leader of an elite SHIELD team.
Amusingly, the brief scene of Yo-Yo in action showed her wearing a red jacket (similar to Flash, DC's resident speedster hero), and the music that played was reminiscent of DC's The Flash. It's an entertaining nod, and - given the Multiversal themes in The Flash - fans will no doubt like to pretend DC and Marvel are all part of the same Multiverse. The comics routinely make just that kind of allusion, so it's fun to see Agents of SHIELD in with this.
Melinda, Daisy & Coulson's Futures After Agents of SHIELD
The rest of the SHIELD team are living out their own "Happily Ever Afters." Quake is one of SHIELD's galactic ambassadors, and she's shown on a tour of duty in deep space on Zephyr Three. Her team include her sister Kora as well as Sousa, and the relationship between Daisy and Sousa is apparently going well. Having Quake perform off-world activities, it's theoretically possible she could one day be instrumental in creating SWORD - something the MCU movies are already doing.
Melinda May is now head of the new SHIELD Academy, the "Coulson Academy," and one of her students is Flint - the Inhuman from a future timeline who was recreated by the power of the Monoliths in Agents of SHIELD season 6. And Coulson is still wandering the world, reassessing his options, albeit doing occasional favors for Mack - who gifts him a souped-up version of Lola. Given that Coulson's exploits still take place on Earth and see him roaming without direct involvement in SHIELD, if a spinoff were ever to happen, following Coulson could be the best option. The SHIELD team has broken up, each member now living their own separate lives, but they will always care for one another and each other.
Agents of SHIELD Can No Longer Exist In The Main MCU
The Agents of SHIELD season 7 finale is a beautiful and poignant episode, but its ending will be bittersweet for fans - simply because there's no way the show can still be considered part of the MCU. The timeline is just too different to the mainstream MCU one; the 2020 seen at the end is one of rich and vibrant hope, when in the movies 2020 was partway through the "Blip," the time when half the life in the universe had been erased by Thanos. There's no way a resurgent SHIELD would have sat out Avengers: Endgame, and they'd have also taken point in Spider-Man: Far From Home as well. So it looks as though Marvel TV's flagship series has officially consigned itself to a separate timeline to the movies, explaining why it became increasingly distant from them.
This doesn't necessarily mean Marvel Studios can't bring the stars of Agents of SHIELD into the MCU, of course. The show's use of the Quantum Realm establishes that, while this series doesn't exist in the main timeline, it does exist as part of the same Multiverse. Marvel Studios is set to explore the Multiverse in the playing Quake in the movies. So the sad truth is that this probably is the end of the road for Agents of SHIELD, the spinoff series that blazed its own trail and built its own wonderful mythology.