As one might expect, not everyone made it out of the series finale of Timeless fully intact, and should the actors return to reprise these roles one more time, they will be doing it at least one or two hands short.
If it's any consolation, the death was not only heartfelt...but tied into the story in such a way that it absolutely justified itself.
Spoilers ahead for tonight's two-hour finale event of Timeless.
In the first hour of the finale, the team's mission to save Rufus is a success -- but not necessarily because of anything that we see on-camera.
When Rufus first arrives, he does not realize that he was ever dead to begin with. It turns out that Flynn had traveled back in time to save him from his death in 1888 by making sure that Rufus never took the job. This means that Jessica is lost forever, and that Garcia Flynn -- who was married to Future Lucy in at least one timeline -- dies stranded in 2012, shortly after having the chance to see his family one last time.
His death rewrites a lot of history, allowing Rufus to continue his relationship with Jiya (although it is complicated somewhat by the differences in their life experiences), and Lucy to end up happily with Wyatt.
Flynn's story is a complex one; he began the series as the principal antagonist, stealing a time machine and manipulating history in order to take down Rittenhouse, who had killed his family and framed him for it. As more and more of the truth of his predicament became clear to the team, they were able to sympathize with him in spite of some of the awful things that he had done. In the end, he sacrificed himself to save Rufus, who in turn managed to save the rest of them when they were tied up in the Old West.
The finale was, surprisingly, Flynn's story. It told of his redemption, his death, and ultimately his origin. At the end of the episode, the team -- now retired -- reunited one last time, so that Lucy could travel to Christmas Eve 2014 and provide Flynn with her journal -- the very thing that had guided his misdeed from day one. Originally, of course, when he said that he had received it from a future version of Lucy, the team had been skeptical...but now the particulars are clear to the team as well as the audience.
Of course, in the event that there is another movie or a miniseries or some other form of continuation, who is to say that Flynn won't return -- either as an ally or an enemy? Time travel can be...confusing.