One Piece does this once per arc; after thwarting the villain's plans or ending his reign of terror, the Straw Hats sail away (Sometimes with a Navy battleship in hot pursuit) from whatever place they stopped at, with some We Will Meet Again mixed in occasionally. It's even more heartstring-tugging when a new crew member is saying goodbye to their loved ones as they join the Straw Hats on their adventures.
Yu-Gi-Oh!: Does this with the titular character. The spirit of the Pharaoh, Atem, has regained all his memories and faces one last trial to determine if his fighting spirit can finally rest from the burden of defending the world. He is then able to take his rightful place and rejoin his family after 3,000 years in the Afterlife.
D.Gray-Man: Allen pulls this in chapter 205 after he discovers that Apocryphos is at the new HQ and that his inner Noah is slowly taking over his body, after saying goodbye and confessing to Lenalee. She doesn´t take it well.
Spike Spiegel from Cowboy Bebop. He leaves the Bebop one final time (much to Faye's dismay) to confront his past and Vicious.
And more importantly, The DigiDestined in the last episode. Of course, Kari and T.K. are back for Digimon Adventure 02, and most of the others stay somewhat in contact with the Digital World by helping the new crop of DigiDestined.
Both the anime adaptation and the manga end with Kenshiro leaving his sidekicks Bat and Lin to wander alone.
The very first story also has a moment like this, when Kenshiro leaves the village after saving Lin from Zeed.
This trick is being pulled half-way through the Air anime, where Michiru disappears after Minagi's mom starts remembering her surviving daughter, since Michiru is a fragment of a dream created by Minagi and a manifestation of how Minagi sees her deceased little sister. It still doesn't really explain though why she had to just vanish, especially since she first hangs around for still another day after her nature is revealed, during which Minagi's mom accepts her as her daughter's friend. Obviously the makers of the series wanted to squeeze as many tears out of it as possible - as if the ending wasn't sad enough already.
And then it was suddenly subverted when we see Minagi's half-sister, who looks exactly like a younger version of, and is also named, Michiru. Contrived Coincidence? I think not.
Layla Ashley in Avenger. After defeating the unbeatable Big Bad, resolving her personal problems, and bringing about a new age of prosperity to the entire planet, no less.
The original Reinforce in Magical Girl Lyrical Nanoha A's. Oh, c'mon, do you really think the lead girls wouldn't be able to befriend the crap out of her defensive program anytime while blindfolded and with their hands tied behind their backs?
They really couldn't. It was annihilated completely.
Fate also does this at the end of the first season, but it's made clear that she and Nanoha would see each other again and the first episode of A's shows that they kept in contact during the interim.
Azumanga Daioh: Done by Yukari in the final episode, where she shares a few parting words with her students, following their graduation ceremony. The girls express their heartfelt gratitude and bow as their former homeroom teacher takes her leave.
In Demon Slayer: Kimetsu no Yaiba, after losing everything, his family, his slayer companions who turned against him for "letting" Muzan and Tamayo go, and twin brother who betrayed the Corps to become a demon, Yoriichi finds the Kamado family ancestors, a cozy family who gave Yoriichi his last remainder of a place to call upon friends; Sumiyoshi is the last person Yoriichi confides his worries in, telling his whole life story and tragedy, but soon Yoriichi feels he can't stay near such a nice family any longer, Yoriichi then part ways with them to never see each other again, afterwards Yoriichi devotes the following sixty years of his life in a personal atonement war against demonkind, reasoning he doesn't deserve any personal happiness, he was born so strong solely to kill demons, anything besides that is straying from the path Yoriichi believes he should have followed all along.
The Secret of Twilight Gemini: After Lupin has exposed Jean Pierre and foiled his schemes, the fabled Geltic Treasure is finally revealed. Lara asks him to stay with her and continue to help her restore the Geltic Tribe to its former glory, but he gently declines, by telling her he had other engagements to keep. Though he promised he'd always remember her and their time together, in Morocco.
Anthy Himemiya in Revolutionary Girl Utena, after Utena is ret goned for saving her. Then she calmly changes her clothes, lets her hair down, goes to Akio's office with Chu-Chu on her shoulder and her travel bag in her hands, tells him she's leaving Ohtori to find Utena, and finally is able to take command of her own life. The last time she's seen, she and Chuchu are happily Walking the Earth, hoping to meet up with Utena someday.
Manatsu and Kai from Uta∽Kata return in the OVA just to invoke this trope.
Parodied in the School Rumble manga. Eri invites Harima to her house overnight to work on the school album. To get him to reveal his feelings, Eri's butler cosplays as a character from Harima's favorite show and fights him. Harima leaves the house without revealing his feelings because that's how the episode ended.
Chao Lingshen, the very, very sympathetic "villain" of the Mahora Fest arc in Negima! Magister Negi Magi, returns to her own time after her plans fail. The reasons she gives are very vague and suspect (she claims she has no reason to stay in this time, despite some very clear evidence to the contrary) leading to at least half the fanbase wondering if she really did return...
Setsuna also tries to pull this, feeling that she doesn't belong now that Negi and Co. know she's half-Tengu, but gets a lecture from Asuna and decides to stay.
In Journeys, a Pichu comes to this decision when he becomes too big to occupy a Kangaskhan's pouch together with her joey, leaving while the two are asleep. The selfless act partially prompts his evolution into the Pikachu that would eventually become Ash's.
Mewtwo and his clones leave the humans and Pokemon in peace at the end of Mewtwo Strikes Back.
Entei almost says this word-for-word in the end of Spell of the Unown as his illusion was disappearing.
In Den-noh Coil, Isako simply leaves town and gives Yasako one last phone call, telling her they might meet again. Considering through how much trouble Yasako went to save her that's quite egregious—but Yasako actually takes it very well.
Kino's Journey: Kino's modus operandi. Reach next town, stay for three days and two nights, then gone. The number of times I Choose to Stay is even considered could be counted on a single hand.
At the end of Kurogane Communication, Haruka and Katano leave their robot families on earth behind to look for the last human survivors on Mars.
At the end of Code Geass: Nightmare of Nunnally, Lelouch, having become the Demon King in C.C.'s place, is forced to leave his sister Nunnally after saying goodbye to her.
For the original Code Geass, fans who refuse to accept the Word of God statement that Lelouch was killed in an attempt to claim this is what happened instead, usually saying that he and C.C. are now Walking the Earth together. The sequel movie which is actually set in an Alternate Continuity shows that this is the case for him and C.C. after saving the world once again.
At the end of GaoGaiGar, Mamoru tearfully says goodbye to everyone as he blasts off in Galeon to eradicate any possible Zonder that may evolve in the galaxy, giving new meaning to the ending sequence we've been watching for the past 40+ episodes.
Rappi Rangai both parodies this and plays it straight; inevitably, protagonist Raizou ditches the current 'princess' he's helped save, usually scrambling to pull this trope off while in tears due to believing he's been rejected or some similar reason. Played straight when the princesses don't actually want Raizou to leave, but he cuts out of there before any of them could say so.
In Risky☆Safety, Risky and Safety successfully beat destiny and reunite Moe with Yuya... but then tell her they have to go to their respective homes now to await punishment, telling her they'll always be her friends as they turn to light and vanish. But don't worry, it turns out that their punishment is to remain apprentices for nearly a century longer, which means being sent back to Earth—they use it as an excuse to stay with Moe.
In My Hero AcademiaIzuku suddenly drops out of U.A. High after the devastation of the hero society. Now that All For One and Tomura Shigaraki are on his trail, Izuku abandons his friends in a bid to protect them.
Ginko in Mushishi at the end of every episode. Justified in that he's an attractor of the troublesome creatures who cause problems for the humans in the series. For this reason, he'll never be able to settle down in one place.
In the final episode of Eureka Seven, the way Renton left the Gekko and Holland commented that he has graduated from Gekkostate.
In Fresh Pretty Cure!, now that Moebius's reign of terror is over and Labyrinth is a safe place to be again, Setsuna, Hayato, and Shun return to Labyrinth, though it's implied that they can come back to visit the Cures any time they want.Which they do. At least with Setsuna.
Subverted in Is This A Zombie?. Eu tries to bail out on the group in episode 9 following an incident where Yoruno forced some very heavy-duty emotion out of her, leading some pretty big shit to nearly go down, but over the next two episodes she decides she can't stay away forever, especially not from Ayumu, so in episode 11 she tells him she'll always be with him, no matter what.
Manga-only example: Mon Colle Knights. At the end of the last chapter, the Knights use the Monster Items to revive Gren, at the cost of losing the items and causing the portal to fade. Before leaving, they mention that they will never be able to visit Mon World again, though certain things afterwards suggest that, in fact, they do. (The anime ends with a new quest for six new Items beginning after the defeat of Reda and Oroboros.)
At the end of A Little Snow Fairy Sugar, Saga loses her ability to see fairies anymore, and explicitly states that she never saw any of them again after Sugar found her Twinkle. Would not have been as contrived if it was just a matter of Sugar having to start her journey as a full-fledged Snow Fairy, with the chance that they'll meet again someday.
After the climactic last battle of GUN×SWORD, Van of the dawn walks off without saying goodbye to most of the good guys, presumably out of a need to figure out "what next?" It's a poignant ending. But the tearjerking is assuaged because the last scene of the series shows him being reunited with Wendy years later.
Riruka from Bleach, in manga chapter 479. She leaves Urahara Shoten without saying anything, then uses her powers to leave Karakura as she thinks of Ichigo, Chad, and Orihime, thanking them for their friendship. Then she returns in the final arc, having been recruited by Urahara.
Technically she never left as she's now, in her words, "everywhere at once." However, only magical girls who are about to die/become witches can see her in their final moments, so it counts. She even spends her last moments with Homura apologizing that she has to go.
Madoka: I'm sorry, I have to leave now. Everyone's waiting for me.
Akiko, Taka and Junichirou from Kasei Yakyoku. The three leave Tokyo few after the Great Kanto Earthquake: Taka and Junichirou take a boat together to abandon the Yakuza, whereas Akiko leaves to live her own life.
In the Pita-Ten manga, this is inverted to But Now You Must Go when Kotarou accepts that even though he loves Misha, he can't keep her with him and has to stand on his own two feet, and asks her to remove his ability to see the supernatural, and therefore his ability to see her.
In the series finale of Transformers: ★Headmasters, after ensuring that the Decepticons can never return to Earth, the Autobots leave as well, with the Witwicky family bidding them a final farewell.
In Getter Robo Armageddon, the original Getter Team sends the Shin Getter team back to their universe so that they can protect it while the old team faces down the Invaders for all eternity.
Momiji returns to the God World after completing her task at the end of Good Luck Girl!
In Sailor Moon, filler villains the Makaiju and the two aliens Ail and En depart at the end of their arc, having earned their second chance from learning what love is.
This is the first scene of Aesthetica of a Rogue Hero. Akatsuki Ousawa was a human who ended up in the Magical Land of Alayzard. He defeated the Demon King and saved the land, then decided to return to Earth despite Queen Listy El Da Sherfied, who had fallen in love with him, begging him to stay, although he promised he would return one day. However, his reason is that he swore an oath to protect the Demon King's young daughter Myuu, and felt that she would be safer on Earth. The rest of the series is their adventures on Earth. He does return to Alayzard a few times.
Julia Asuka and Ru-Kain pull this in the Blue Comet SPT Layzner third OAV, returning to Grado together after Julia unlocks the MacGuffin that lets them do so, so they can start working on peace there.
At the end of Naruto, Sasuke leaves to Walk the Earth after reconciling with Naruto. According to Word of God, he's leaving to investigate the origins of Kaguya Otsutsuki and her plan to revive herself to prevent a similar thing from happening again in the future. Interview available here.
In the final episode of Wish Upon the Pleiades, the President, having repaired his spaceship, flies off into dimensions unknown. The girls also must return to their separate universes, although it's heavily implied that they'll meet each other again within their own timelines.
Goku pulls this more than a few times. In his childhood, he leaves his friends several times to either train, to look for the 4-star Dragon Ball, or go after someone. He also leaves behind the people he saves like Suno and Upa, some who never see him again. At the end of the Cell Saga, Goku chooses to stay dead since most of the villains in Dragon Ball Z came to Earth because of him. He does it again at the 10-year Time Skip after the Buu Saga; he decides to live in a village with a boy — the Reincarnation of Majin Buu — to train him to become a martial artist. Dragon Ball GT ends with Goku riding away on Shenron's back and not being seen for one-hundred years.
Dende leaves with the rest of the Namekians to look for a new world at the end of the Frieza Saga. He comes back near the beginning of the Cell Games.
After everything with Cell is dealt with, Future Trunks returns to his timeline and take care of the remaining androids. He returns inDragon Ball Super. Then he does it again at the end of that arc, moving to a new timeline entirely.
Yuri!!! on Ice: Yuri tries to invoke this by telling Victor that he'll be retiring after the finals. It backfires horribly; this actually prompts Victor to break down in tears and accuse Yuri of being so selfish.
Sakura Quest: After Yoshino spends an eventful and emotional year fulfilling her contract of helping to revive the town of Manoyama as the "Queen of Chupakabura," she decides to leave because she doesn't want to "surrender to the feeling of being at home."
In Tenchi Universe, the girls leave Tenchi after their journey to Jurai to clear their names. As it turns out, life without Tenchi is totally boring and they all race back to Earth.
Okko's Inn has this in the ending. After Okko learns all she can and comes to terms with her parents' deaths, the ghosts leave to be reborn in human bodies.
In Mini Moni The Movie: Okashi na Daibōken!, thanks to Queen Nakajalinu's magic the cake castle becomes as big as an actual castle on the inside, with multiple floors and a dungeon.
Alisa of the Silver Hair ends with Alisa sailing away, telling Mio she'll return when she can once again call herself "Alisa Honjou."
The Vision of Escaflowne utilizes this trope at the end when Hitomi returns to Earth, despite a) having a magical pendant that lets her instantly teleport between Gaea and Earth at will, b) returning to Earth not two episodes before but returning to Gaea to be with Van, and c) the strength and purity of their young love defeating the Big Bad and restoring peace to Gaea not five minutes before.
Wolf Children: Ame in the ending, where he chooses to live as a wolf and rule the forest in his deceased teacher's place.
Hell Teacher Nube ends with Nube and Yukime transferring to Kyushu to protect a new group of school kids from the supernatural. Before departing, he leaves the duty of protecting the Domori students to Tamamo.
Queen Millennia: In the end, Yayoi and Larela make up and decide to leave with La-Metal, with humanity resettling on the new Earth.
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