The X-Files: Season 9 Mytharc
The series's mytharc proper ended with Fight the Future and the sixth season eps "Two Fathers" and "One Son", before being rebooted in Season 8 to surprisingly excellent results; one could tell Chris Carter intended Season 8's mytharc to be the show's last hurrah, in which he threw every ounce of pathos and suspense he could into a series that had halfway lost one of its major stars and now revolved around a potentially disastrous pregnancy macguffin. It all ended on an exciting, solidly satisfying season finale that would have (and should have) served as the series finale proper.
But then Fox decided to continue the show with or without Chris Carter, forcing him back into the show runner chair out of pride, and then producing the series killing, reputation destroying Season 9, in which the show's grandly epic and ambitious mytharc takes a shocking nosedive into complete unwatchability. After building up an awesomely-ludicrous-yet-ludicrously awesome tale of alien invasion, encompassing all of Earth's history, and the myriad squabbling political factions of humanity trying to either aid, stop or sidestep it for eight seasons, the final season's mytharc revolves around the most unimaginative, boring scifi concept imaginable: supersoldiers. Even worse, the show's most groundbreaking and dynamic element, its cinematic scope and high production values, have been slashed. Gone are the visually stunning set pieces the show produced in the past; now all the "action" is confined to apartments and office rooms while rehashed suspense plots unfold, and the glossy, stylized cinematography is gone. For the first time, X-Files looks like what it always so gloriously avoided being -- just another TV show.
And while the much hated series finale has most of these flaws, as well as the impossible task of effectively wrapping up nine seasons worth of convoluted sci-fi conspiracy intrigue, it at least fortunately finds something of the groove that made the first eight seasons work -- the emotional connection to the characters that also evaporated in Season Nine, as Duchovny was gone, Gillian Anderson reduced to a mere supporting character, and Robert Patrick and Annabeth Gish trying hard but never escaping their shadow. It starts out awful, gets progressively better if only for the way Carter outlines the entire mytharc in broad cliffnotes format (it all does hang together, more or less, contrary to common consensus), and ends strong with a tearjerker of a scene between Duchovny and Anderson, alone, on the run, and facing a bleak future, but finally reunited. Given the rest of the season, it could have ended a lot worse.