Special episode, a sequel to the events in Pokémon: The First Movie (while it was aired as a side-story episode in Japan, it was given a direct-to-video release in America).

Giovanni, the leader of Team Rocket, has caught a clue to the location of the powerful Pokémon Mewtwo and has sent an agent to find him. In the meantime, Ash & co. are passing through the Johto region when they encounter a woman who told them about the vitalizing water of Purity Canyon...coincidentally, Mewtwo's new location. Soon, an all-out battle between Mewtwo's clone Pokémon "family" and the forces of Team Rocket breaks out, with Ash and his friends caught in the middle.

This special provides examples of:

• Badass in Distress: Mewtwo again.
• Badass Normal: Domino doesn't seem to have any Pokemon of her own, but that doesn't stop her from fighting anyway.
• Bad Taste Call-Out: The mineral content of the Purity River's water makes it widely considered healthful and delicious... except to Ash, who thinks "it kinda tastes like something's been swimming in it." Misty and Brock promptly lay into him for having no taste. He concedes the point when Pikachu and Togepi try a sip and both love it.
• Big Damn Heroes: Mewtwo does this four separate times in the movie. First, he saves the below-mentioned Bus Full of Innocents; second, he stops clone Pikachu from delivering a No-Holds Barred Beatdown to Ash's Pikachu; third, he stops Giovanni just as his enemy is about to capture both Pikachu and Meowth, then frees all the other clone Pokémon; and finally, he saves the healing spring and lake from probable destruction by Giovanni, teleporting the whole darn thing underground.
  • When everyone, including the all-powerful Mewtwo is captured and it looks like Team Rocket has truly won, the local bug Pokemon converge on and furiously attack the Team Rocket base, freeing everyone in the process and resetting the playing field. Lampshaded by Meowth's ominous words: "They're coming... and they're very angry."
  • Surprisingly, Meowth comes into this as well: other than helping the heroes in freeing Mewtwo, he also convinced Mewtwo not to erase everyone's memories because the journeys of the clone Pokemon involve learning about their past to reflect on their future; even Ash compliments Meowth for providing such a good reason.
• Bitch in Sheep's Clothing: Domino might look innocent at first: but she's actually a villain.
• Bittersweet Ending: Mewtwo is free to discover his place in the world, but he is alone again, and potentially will never see his clones ever again with the exception of Pikachutwo and Meowthtwo that went with him.
• Born as an Adult: Sort of. A Nidoqueen and a Rhyhorn have offspring, some of which are baby Rhyhorn, and some of which are tiny baby Nidoqueen. Normally, if Nidoqueen were able to breed in the games, they would be Nidoran. It could be assumed that because the Nidoqueen and Rhyhorn are clones, this is how breeding works for them, but none of the characters question this despite not knowing that they're clones at that point, so either it's a complete oversight or that's just how breeding works in the anime.
• Breaking the Fourth Wall: James mentions that "this feels like a sequel to a movie I missed."
  • Also, at one point Domino looks directly into the camera, winks and says (apparently to the audience) "You just never know! It may look innocent, but a friendly face could be hiding our fiercest foe!"
• Bus Full of Innocents: Mewtwo saves one at the beginning of the movie, justifying it by saying he didn't want to risk exposure if there was a search for survivors by rescue parties.
• The Cavalry: When things look at their bleakest, a monstrous swarm of furious Bug Pokémon attack and overwhelm Team Rocket.
  Meowth: They're coming... and they're very angry.
• Clone Angst: All of the clones to an extent, but mainly Mewtwo and the Pikachu clone.
• Crazy-Prepared: Mewtwo's hideout is equipped with some sort of flatscreen he uses to monitor the area and a jail cell underneath the mountain for potential intruders.
• Crucified Hero Shot: Mewtwo, who is held in this position while being held captive by Giovanni's robots. After offering himself up to be tortured in his clones' place in order to save them.
• Cuteness Overload: Domino can't help but find the baby clone Pokémon adorable.
• Darker and Edgier: Mewtwo Returns was rated PG, presumably for the aforementioned whiskey, the philosophical themes, and generally having the same dark and serious tone as Mewtwo Strikes Back.
• Don't You Dare Pity Me!: The cloned Pikachu swats away its original at one point.
• The Dragon: Domino is very high in Giovanni's favor.
• Dub-Induced Plot Hole: Near the end, Ash says to Mewtwo "This time we'll both be able to remember," even though Mewtwo never informed him that they met previously. This line isn't in the Japanese version.
• Electric Torture: Mewtwo, yet again.
• Epic Fail: Domino fights her way past a trio of Scyther and then flawlessly flips over them... only to slip on a wet floor and get her head stuck inside a pail. Doubles as Irony, since she had previously forced Jessie and James to mop said floor.
• Evil All Along: Domino initially appears to be a cute and sweet college girl and Cullen's assistant, but when Jessie and James make the scene, she reveals herself to be an elite Team Rocket agent working directly under Giovanni himself.
• Eviler than Thou: Domino proves to be as such to Jessie, James, and Meowth, popping their balloon while expressing disgust at their bumbling ways and declaring them a disgrace to Team Rocket.
• Frothy Mugs of Water: Actually part of the story in this case—Purity Canyon's water gives people and Pokémon something akin to a sugar rush...
• A Glass in the Hand: Giovanni does it twice, first with a glass he's drinking from, and to a walkie-talkie (!) near the end of the movie.
  • A Glass of Chianti: Or what looks like whiskey, in this case. Surprisingly untouched by 4Kids for the dub.
• Green Aesop: Don't pollute water, or you'll be attacked by hordes of angry insects.
• Healing Spring: Purity Canyon.
• Humans Are the Real Monsters: Although no longer wanting to exterminate humanity, Mewtwo still has a low opinion of "Man" and the other clones seem to have adopted his mindset. It's justified on the fact that Giovanni and Team Rocket are planning to capture Mewtwo and the clones for their own ambitions.
  • Ironically, Mewtwo did have a human friend once.
• Improvised Umbrella: Early on when Ash and company get caught in the rain, Brock decides to use his frying pan... as a drying pan.
• I Will Punish Your Friend for Your Failure: Giovanni is no fool. He knows testing the limits of Mewtwo's power is futile, so he despicably threatens to murder his clone brethren, and all the nearby Pokemon, if he does not cooperate and serve him.
• Kick the Dog: Giovanni actually snaps at his precious Persian to be quiet. ^note Though originally, he is asking what the matter is.
• Know When to Fold 'Em: Upon Giovanni and Team Rocket being erased of their memories (with the exception of Jessie, James and Meowth), Domino wonders what they are doing before advising Giovanni that they and their forces should leave before the authorities find out. Despite having a strange feeling about this, Giovanni agrees to Domino's suggestion:
  Domino: I don't know any more than you do, but we don't get out of here now, it won't be secret.
  Giovanni: Hmm, we should withdraw forces at once. It's strange, but I have the feeling that I have been UTTERLY defeated.
• Laser-Guided Amnesia: Mewtwo does this to all of Team Rocket (as well as Luna and Cullen) except for Jessie, James, and Meowth in the end, though one can't help but wonder why he didn't think to do this beforehand. Subverted with Ash and co., as Mewtwo allows them to keep their memories, and seeing as Ash says, "This time we'll both remember," Ash probably figured out that they've met Mewtwo before and just can't remember it.
• Little Miss Badass: Domino of Team Rocket, who is only around Brock's age. Also, a Badass Normal.
• Love Redeems: Sort of. He was actually one of the good guys, but Cullen Calix was obsessed with studying the spring of Purity Canyon, even if it meant harming it. But once Mewtwo wipes his memory, he realizes that he's in love with Luna and that this is more important than research, so he settles down with her rather than pursue his ambitions.
  • In a non-romantic sense, Mewtwo coming to love his temporary home and his clones gave him as big of a change of heart as Ash's selfless sacrifice did.
• Near-Villain Victory: One of the biggest in the series.
• Never Say "Die"
  Mewtwo: I would sooner leave this world than serve you.
  Giovanni: I suggest you reconsider your opinion. If you choose to defy me, your fellow creations will all be used in our experiments and will certainly leave this world.
• Obfuscating Stupidity: Teenage girl Domino acts like a typical Dumb Blonde before revealing that she's an incredibly capable agent of Team Rocket.
• Offscreen Moment of Awesome: A massive battle undoubtedly takes place while Ash is taking Mewtwo to the spring between Brock and Misty vs what looks like every Team Rocket operative. It's going to start up and...we cut to Ash dragging an injured Mewtwo up the stairs. We NEVER see any of the battle.
• Ojou Ringlets: Domino's hair is styled this way.
• Papa Wolf: Mewtwo, as noted below, behaves much like a father figure to his clones. And he gets very annoyed if you mess with them.
• Parental Substitute: Mewtwo acts much like an anxious father regarding the other clones, and debates whether he should let them set out on their own or if he should make them stay where he can guard them.
• Perky Female Minion: Domino, who almost fits the criteria for Perky Goth...except for not actually being a Goth.
• Perma-Stubble: Cullen seems to have a bit of this going on.
• Pet the Dog: Domino thinks the baby clone Pokémon are cute and even holds and pets one... She still has no qualms knocking out their parents with electric tulips.
• Pragmatic Villainy: Domino advises Giovanni not to continue torturing Mewtwo because Mewtwo is valuable, and it would be a waste to kill him. If they destroy him, it'll take years to create another clone. Giovanni acknowledges this, but doesn't care. It's become a battle of willpower, and Giovanni is determined to prove his is the stronger.
• Properly Paranoid: The security cameras and prison cell indicate that Mewtwo believes humans are bound to find them eventually. He's right.
• Psychic Link: In the end, Mewtwo for the first time, expresses genuine heartfelt gratitude. To Ash and his friends no less, for saving his clones and himself, and help him see his own self-worth. He establishes a psychic link with Ash, which occasionally echoes this appreciation whenever he thinks of him.
• Red Baron: Domino, AKA The Black Tulip.
• Redemption Demotion: Subverted with Mewtwo, Giovanni simply finds his weak point.
• Reformed, but Not Tamed: Mewtwo is no longer a world-destroying monster...but he still has a deep distrust of the outside world.
• Right-Hand Cat: Persian, as usual.
• The Slow Walk: Mewtwo as he submits and walks into the capture/torture machines. The real shocker, though, is the reveal that Mewtwo is capable of walking in the first place.
• Valley Girl: Domino speaks like this in the dub before The Reveal that she's part of Team Rocket.
• Villain Has a Point: While Meowth is no saint Pokemon due to his affiliation with Team Rocket, he objects to Mewtwo's plan of erasing everyone's memories for a very good reason: the clone Pokemon have every right to learn about their origins and that erasing everyone's memories will deny them that opportunity to continue living their own lives, leaving them more heartbroken. Even Mewtwo, Ash and the heroes agree with Meowth on this.
  Meowth: It's only natural to wonder about who and where you came from and someday these little ones are gonna want some answers. Only there won't be any, not if you gonna make everybody forget! So what if their parents were clones? They're all living creatures. They deserve to live, and they deserve to know about themselves as much as you, or me, or anybody does! That's what we think.
• Villain No Longer Idle: Giovanni takes an active role as the Big Bad; notably, this is the first time he's met Ash and co.
• Walking the Earth: Mewtwo decides to embark on this at the end....and with a snazzy cape to boot.
• What the Hell, Hero?: A subtle one; Ash needs to save Mewtwo's life by throwing him into the spring. Cullen then tells him not to because it might contaminate the spring, which he's obsessed with studying, and that humans need the springs' nutrients and healing properties. Ash's response is to look pissed at Cullen's selfishness, snap at him that Mewtwo needs it more, and throw Mewtwo in anyway.
• You Are a Credit to Your Race: Mewtwo wants to know the reason why Ash is trying to save him. Ash replies you don't need a reason to help another. Mewtwo then considers Ash unique, one-of-a-kind. Ash informs the genetic Pokemon, everyone is unique, and that includes him too.
• You Bastard!!: A family-friendly example, When Giovanni subtly threatens Mewtwo's clones, a disgusted Mewtwo angrily replies: "You are despicable"
• Zerg Rush: By various Bug-type Pokémon after Team Rocket occupies Mewtwo's island home. By the way, Bug is super-effective on Psychic. Until the Psychic gets its turn.