Denouement Episode

The Story Arc has reached its end, and the main characters face off the Big Bad. He's dead, the team rejoices, the end.

Hey, there are still a few rather minor loose ends... oh well, they will be taken care of next season.

...wait what? The Grand Finale was in fact the penultimate episode and there's one more episode left?

This is when the main Story Arc is resolved in the second to last episode, and the Season Finale acts as a Denouement and deals with the loose ends, sets up the next season or is a Stand Alone Episode.

The trope obviously does not apply when the entire season consists only of standalone episodes without clearly recognizable story arcs.

See also Denouement. Related to Where Are They Now? Epilogue. If the episode takes place far in the future instead of the usual timeframe, it is a Distant Finale.

Anime and Manga

 * Sailor Moon S (consisting of episodes 90–127) had a Grand Finale in episode 125. Episode 126 was the Denouement; episode 127 was the Sequel Hook.
 * Negima!?'s last two episodes were this.
 * This is standard procedure for the Magical Girl Lyrical Nanoha series. The big battle ends during the penultimate episode of the season while the last episode deals with the aftermath of the incident, showing what the various characters are doing now and where they plan to go in the future.
 * The penultimate episode of Ghost in the Shell: Stand Alone Complex's first season was a big cliffhanger—but then the next episode involves all the characters, post-Time Skip, wrapping up all the loose ends via several conversations.
 * Both seasons of Clannad resolve their respective halves of the overall narrative by the penultimate episode, with the de facto last episode(s) being either recap, Flash Back or WAFF episodes.
 * Fullmetal Alchemist: Brotherhood's final episode comes post Big Bad fight, and features emotional resolutions for most of the characters.
 * The last Fruits Basket book is all resolving people into marriage, college, and other ways to settle their lives forever.
 * The Dragonball Z anime finishes off the final villain with time to spare; the last few episodes are light filler followed by a Time Skip and a very brief Tournament Arc to wrap things up.
 * Monster's final episode was like this.

Live-Action TV

 * The series finale of Sliders: after having defeated the Big Bad of the final season, Dr Oberon Geiger, the Sliders come to a world where they are given the means of liberating universes from the Kromaggs, the Big Bads of the previous season.
 * The fourth season finale of Buffy the Vampire Slayer. Adam is dead, and the episode is about Willow, Xander, Giles and Buffy sleeping. And dreaming.
 * The fourth season finale of Angel. The Big Bad was defeated in the previous episode, and in this episode Angel Investigations must decide if they join Wolfram & Hart. But there's still Connor...
 * Coincidentally enough, another fourth season finale. Of Charmed this time. All of the incarnations of the Big Bad were permanently and definitely killed, and in this episode the Angel of Destiny gives the Charmed Ones a chance to give up their powers and their destiny as witches.
 * The sixth season finale of That '70s Show. Eric and Donna's wedding (the main story of the season) was called off in the previous episode, and this episode is mostly about Kitty finding out Bud isn't Hyde's father.
 * The second season finale of How I Met Your Mother only reminds us of the season's Story Arc because the main characters are celebrating Lily and Marshall's wedding (who are married since... right, the penultimate episode), but it's mostly about Ted and Robin's breakup.
 * The fourth season finale of Babylon 5, "The Deconstruction of Falling Stars". The Vorlons, Shadows, and other First Ones have buggered off beyond the rim of known space and left the younger races to their own devices, Earth and its various colonies have been liberated from Clark's regime, Sheridan's found himself at the helm of the new Interstellar Alliance. Sounds like everything's already wrapped up, right? Well, it is, and the whole episode can be described as a series of Flash Forwards.
 * Which is more Real Life Writes the Plot as the series was on shaky ground and JMS scrambled to write something that would both satisfy the fans if it wasn't renewed and provide a plot for another season if it it was.
 * Actually, the true ending of season 4 was the season 5 ender "Sleeping In Light". As the show was uncancelled at the last minute at the end of S4, JMS had to write a filler episode. If you want the series to end on a beautiful note, skip Deconstruction and season 5 and put on Sleeping. Warning: this episode will leave you in tears.
 * A staple of Takara's Tokusatsu series. Madan Senki Ryukendo, Tomica Hero Rescue Force and Rescue Fire all indulge in it.
 * Slightly cheating, but "Moebius", the two-part finale of Season 8 of Stargate SG-1 fits the bill. The previous three episodes had resolved essentially all of the series' story arcs up to that point. "Moebius" was a pretty standalone pair of episodes, though it was very good.
 * It was actually a much bigger part of the spin-off's Stargate Atlantis story arc than SG-1's.
 * Even "Threads" was a bit of a denouement episode, dedicated mostly toward resolving the remaining story threads. "Reckoning" was more of the big Grand Finale that ended the central conflict of the series. So really, there were three episodes after the climax.
 * The final episode of Kamen Rider Double jumps ahead a year after the Grand Finale, showing the audience how the characters are doing and Shoutarou continuing to protect Futo City as a detective and Kamen Rider . It ends on a Crowning Moment of Heartwarming.
 * The climax of One Tree Hill's fourth season takes place in the second and third-to-last episodes, with  The final episode of the season mostly takes place at a graduation party and cleans up loose relationship threads.
 * The second-to-last episode of season 2 of The Vampire Diaries deals with the ritual to break the curse on Klaus. The last episode is about
 * The fourth season finale of Mad Men.
 * The fifth season finale of The Office. In the second half of the season, Michael quits and creates the Michael Scott Paper Company, which is then bought out by Dunder Mifflin. The following episode has Michael deal with the aftermath of the buyout, and in the one after that, Michael uses the MSPC office for other purposes. The final episode however is about Michael and Holly, and sets at least two season 6 storylines in motion, with no reference to MSPC or Jim and Pam's upcoming wedding (which also was an important story arc during that season).
 * The sixteenth episode of the 16-episode South Korean series Strong Girl Bong-soon is over an hour of "What happens next?" after Bong-soon, Guk-doo and Min-Hyeok defeat the Big Bad, including loads of "Where Are They Now?", a wedding, and Babies Ever After -- and the start of the career of Seoul's first Superhero.

Western Animation

 * Teen Titans actually did this for its series finale. The previous episode had wrapped up that season's Big Bad with the Titans forming a giant, Heroes Unlimited team to take the bad guys down in a massive, all-out brawl. Cue a Bittersweet Ending focusing on Beast Boy trying to connect with a girl who may or may not be his Love Interest come back to life.
 * Transformers Cybertron finishes the the main action in End (black hole stopped) and Unfinished (Galvatron defeated.) Then there's one more episode, "Beginning," that shows what's next for everyone.