For most of the series, the couple constantly found themselves literally separated by space and time — so often that Fitz was convinced that the cosmos just wouldn't allow them to be together.
But fans of Fitz and Simmons always knew that they were endgame, and the finale gave the characters a satisfying, well-earned ending.
Fitz was noticeably absent during most of the final season because De Caestecker was filming another project at the time of shooting "AoS." With the actor's limited schedule, Fitz's absence was written into the plot.
In the finale, viewers learned where he was.
Earlier on, the Chronicoms got a hold of Fitz and Simmons and accessed their memories with a machine. Because the pair figured out a way to defeat the Chronicoms and save the team, they couldn't risk their plan being discovered by the Chronicoms.
So Fitz disappeared to an unknown location for his protection while Simmons stayed behind and had an implant put in her body that suppressed her memories and therefore concealed Fitz's location and plan.
In the finale, the couple reunited, though it took Simmons some time to regain her memories and recall who Fitz was. Fitz explained that he was in the original timeline the whole time he was missing.
He said that when the team went back in time, they branched off from the original chain of events and created an alternate timeline. But by entering the quantum, as he did after going subatomic, the agents would be able to jump between the two timelines and defeat the Chronicoms.
Through a series of flashbacks, fans saw that FitzSimmons lived out a happy life together in the years that they spent working on a world-saving solution.
This is also when Fitz built the Coulson LMD, which was created specifically for this final mission so they could all work together.
Fitz always knew that their plan would work, so he and Simmons delayed fixing everything so they could enjoy their time together. They even had a daughter named Alya.
While virtually gathering with the rest of the agents after the one-year time jump, it was revealed that Fitz had retired from S.H.I.E.L.D. and was enjoying fatherhood.
Meanwhile, Simmons was also no longer with S.H.I.E.L.D. but was quietly helping Daisy with an anatomy analysis.