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Fusion Generation II is a sequel to the 2012 fanmade Pokemon game Pokémon Fusion Generation. Developed between 2013-2014, it officially remains unreleased after the series was Screwed by the Lawyers but a beta version started appearing in YouTube Let's Plays in 2018.
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The sequel adds hundreds more fused Pokemon species and many more ways to get them. The story builds on an event from the first game in which a young Ethan witnessed Brendan or May battling. Though much time has passed Ethan (or you can play as Lyra) still remembers that trainer who inspired them to battle and now seeks an even bigger adventure that will span multiple regions and beyond.


This Game contains examples of:

  • Ability Required to Proceed: A new hidden move called Cold Feet is the only way to pass pools of lava.
    • Like in the first game, Brick Break is used outside of battle to get past invisible barriers. The final boss can't be faced until you use it to get into the last laboratory.
  • Aborted Arc: The bad guys targeting Bill along with the revelation that visitors to the island all go missing may seem like one to the player when it isn't brought up again for a very long time, but subverted when it's revealed that they did indeed act on their plot and replaced Bill with an impostor at the very beginning of the game.
    • Arceus and the Mission from God plotline that was a major part of Pokemon Fusion Generation are never brought up in the sequel aside from a reference in the intro sequence
  • Accidental Murder: Played with in the case where Hart, Drayden, and Looker accidentally kill a girl and still carry tremendous guilt, making a pact never to speak of it again. Although it was not intentional on their part, it went more or less how their captain wanted it to.
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  • Adaptation Name Change: N's canonical full name is disregarded and his full name, which gets its own origin story, is stated as N Harmonia.
  • Adaptational Nice Guy: Having befriended the player character, this adaptation of Silver is much softer.
  • Alien Abduction
    • A postgame event has you abducted by aliens, and you can repeat the event and get voluntarily abducted once per night
    Clefable: Alien abduction is such a harsh term. I prefer, "spacecation!"
  • Aliens Speaking English: Subverted. It may seem like the Clefairy are speaking your language when you arrive on the Moon, until the camera pans out to reveal that the reason you understand them is because you're a Clefairy now.
  • All Up to You: Meowth must carry on Team Rocket's quest to avenge Giovanni in Laboratory X after Jessie and James fall through a trap door and leave him with their Fusions.
  • Anal Probing:
    Clefable: Not to worry. Your body is in our space craft for probing. SAFEKEEPING! Yes, "safekeeping" is the word I meant, of course.
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  • Ancient Astronauts: Clefairy who originated on the Moon claim to have had fusion technology for eons.
  • Anti-Frustration Features
    • The rocks in front of the Eterna Galactic Building will never return after you've been inside.
    • If you mess up the Laboratory C puzzles too many times, Dawn will give you a hint that the buttons represent elemental types (but she won't tell you which buttons represent which types)
    • The HM for Fly is available very early in the game. It can be found as soon as you get to the eastern Splicen, as cutting through the maze-like jungle every time you want to go back to the east from the west not to mention navigating the 6 other regions on foot would be especially annoying.
  • Arc Welding: By the time they reach the final lab the stories of Ethan/Lyra and Dawn, Silver and Hart, Ellie and Gray, and Jessie and James have merged and they all bust into Laboratory X together for their own reasons.
  • Awesome, but Temporary: Just as you get to use Rayquaza at the start of the first entry, you briefly have a Lugia at the beginning of this one. This time it's stolen from you, before you can even battle any trainers with it.
  • Back for the Dead: Ellie is apparently killed after returning for a single scene. Subverted when she turns up fine.
  • Becoming the Mask: Lila's personality changes wildly throughout the game as she uses her transformation ability more and more.
  • Big Bad: Ghetsis.
  • Big Bad Wannabe: Gray builds himself up as Dawn's arch-nemesis, but is crushed when they finally meet and she doesn't even remember who he is.
  • Blackmail: Ellie knows Mayor Drayden's big secret and uses it against him to force him to drop out of the race. It backfires, big time, and he wins anyway.
  • Bonding Over Missing Parents: Gray tries to use his own lost mother to relate to Ellie. She responds by bashing him over the head with a bicycle.
  • Book-Ends: Pokemon Fusion Generation begins with the former Champion of Hoenn arriving in Kanto to conquer its Pokemon League and Fusion Generation II ends with the former Champion of Kanto going to Hoenn to defeat its league.
  • Breaking the Fourth Wall: Team Rocket does this with more frequency as the game goes on. Lampshaded by Dawn.
  • Brick Joke: In Pokemon Fusion Generation NPCs dismissed the strange happenings on Cinnabar Island with the phrase "I'm sure it's nothing to worry about!" In Fusion Generation II the Cinnabar volcano has erupted again and an NPC in Viridian laments, "It was...something to worry about..."
  • Captain Obvious:
    Ellie: Well I guess I've been alive as long as I can remember...
  • Cast Full of Gay: Of the confirmed romances or implied ships in Fusion Generation II, heterosexual ones are in the minority.
  • Challenge Seeker: Dawn embodies this trope in the game. It's her motivation for leaving Sinnoh in the first place and traveling around the world getting into battles.
    • Lila is one too, insisting on fighting the player rather than any of the other characters citing their superior skills.
  • Character Derailment: When she first shows up in Fusion Generation II, Ellie is nothing like she was in the first game. Her drastically different behavior is lampshaded by the people of Opelucid City. Subverted when it's revealed that she's not the real Ellie.
  • Character Development:
    • Gray is a self-centered control freak but grows to sincerely care for Ellie and be more considerate of others.
    • Ellie is fiercely independent after being suckered and mistreated by Team Magma but learns to open up.
    • Hart eventually learns to stop running away and returns home to his family.
  • Character Select Forcing: If you choose Cyndavee as your starter it will be less than helpful in at least the first two gyms, and possibly the third gym leaders since his team includes fire and water typing.
  • Chekhov's Gun:
    • Though Rydel won't accept the bike voucher Wally gives you, later in the game the Eterna City bike shop offers to take it off your hands in exchange for an upgrade you'll need to progress.
    • Team Rocket steals Dawn's gym badges at the beginning of the game, and at the end they use them to enter the Hoenn League and ambush the player.
  • Cloudcuckoolander's Minder: Gray to Ellie.
  • Collapsing Lair: Laboratory X begins to selfdestruct after Ghetsis is defeated. Debris falls on Team Rocket, Lila, and N and they nearly don't make it out.
  • Combat Compliment: Like in the Generation V games, important opponents like Gym Leaders will say something, usually a compliment, when they send out their final Fusion.
  • Comically Missing the Point: If you call Ellie on your PokeGear, she messes up the "Liar liar, pants on fire" saying. Gray tries to correct her, but takes it to mean someone's pants are literally on fire and hangs up in a panic.
  • Complete Immortality: Lila, until Bill restores her humanity and changes her back into Alma. Presumably then Mortality Ensues.
  • Continuity Nod:
    • It was a source of surprise and confusion for Pokemon Fusion Generation players when they found a free Staryu in an unattended house. In Fusion Generation II, the owner of the house vows to find her stolen Staryu.
    • Ellie having been part of the team responsible for stealing Bill's house is referenced on multiple occasions.
      • When she first sees the teleporting cottage she asks where all Zubat are, assuming this is still how it's being moved around. This is lost on Gray who tells her she's crazy.
      • There's also a tense exchange about this when she meets Bill for the first time.
  • Convection Schmonvection: Lava is present in many areas, and the move Cold Feet lets you walk on it simply by freezing your feet. You can even go fishing in it.
  • Crapsack World: The Hoenn region is literally sinking into the ocean and the economy is in shambles.
  • Creature-Breeding Mechanic: Fusions can only hatch from eggs if both parents are Fusions. Breeding a Fusion with a regular mon will result in a regular baby.
  • Cryptic Conversation: Every scene with the bad guys plotting. A lot of their conversations will only make any sense on subsequent playthroughs.
  • Curse Cut Short: Ghetsis was going to call Lila an ungrateful...probably not something nice, but is interrupted by the arrival of his son.
  • Dead All Along: The REAL Lila. Though Ghetsis has convinced Alma that she's Lila, she's just a Replacement Goldfish that he created until he could bring back his One True Love.
  • Deadpan Snarker: Meowth, often in response to repeated surprised reactions that he can talk.
  • Deal with the Devil: Ima helps fake her own daughter's death as part of a deal with Lila, with the hope of bringing back her dead daughter Mira.
  • Death Is Cheap: Only characters that died prior to the start of the game (Mira, Blair, and the original Lila) stay dead. The characters that presumably die during the game (Ellie, Gijinka Lila, and Team Rocket) all turn out to be fine.
  • Disappeared Dad: Hart abandoned his family, the player character and their mother, because of his guilt over what he did on the island.
  • Disc-One Nuke:
    • Finding a Mariblitz with Huge Power early on will make the game way easier. The combination of the ability with its stats make it a big improvement on both Marill and Blitzle.
    • You can find the Nidoran fusions Nidopinch and Deinoran as soon as you get to the east side of Splicen Island as well as Moon Stones needed to evolve them all the way to their final forms. You can either get their powerful final stages Flyking and Hydraqueen as soon as level 26, or you can separate them and get your own Flygon and Hydreigon before you get your second badge.
    • There are some OP TMs available early in the game like Dazzling Gleam and Scald that can make the early game a breeze.
  • Does This Remind You of Anything?:
    • Upon arriving to a mysterious island few know about a character goes into the jungle and disappears after hearing whispers from an unseen entity. In the past there was a purge of all the islands' inhabitants and also an "incident" that resulted in strange happenings. Soon laboratories, some abandoned and some active, are found throughout the island including underwater and underground. Eventually it's revealed that a shapeshifting monster has been impersonating one of the protagonists for some time.
    • Character trashes stranger's bike and they end up sticking together.
    • The Psychic from Opelucid City abandoning Swaggy is reminiscent of someone abandoning an unwanted pet.
  • Dungeon Bypass: If you already know the passcode for Laboratory A, it's entirely possible to go straight to the boss.
  • Early-Bird Cameo: Ellie can be spotted in the crowd during Drayden's televised speech.
  • Elemental Rock–Paper–Scissors: The button puzzles in Laboratory C.
  • Endgame+: A seventh region, Kalos, as well as the Moon become accessible after beating the main game.
  • Everyone Is Bi: Eli will tease Ellie about crushing on either Brendan or May from the previous game.
  • Eye Scream: When the International Police blow up Ghetsis the explosion takes out his eye.
  • Fanservice: Lampshaded by Jessie when she shows up wearing a bikini for no apparent reason.
  • Foregone Conclusion:
    • N returning to Ghetsis, since the game is set before Generation V.
    • Drayden's victory in the election, for the same reason.
    • Once again all the Fusions have started being returned to normal after the main game.
  • Foreshadowing:
    • Lila's true identity as a Ditto Gijinka, and also her impersonation of Bill and Ellie are hinted at many times.
      • When Bebe tells Bill it's great to see him, he replies, "Ditto."
      • Lila mentions in cutscenes that she's having fun toying with the protagonists, which won't make sense to the player at the time given that as far as they know they've barely interacted with her.
      • As Ellie, Lila says that Drayden may know her face but has no idea who she really is. She meant it quite literally.
      • Lila appears as Zekrom shortly before the player meets her impersonating Bill for the first time, and as Reshiram shortly before she speaks to Silver for the first time.
      • Lila speaking critically of humankind foreshadows that she is not human herself.
      • In hindsight it's obvious that as Bill, Lila attempted to sabotage the protagonists several times, by trying to keep the storage drive with the stolen Fusions on it, by manipulating the player into visiting Laboratory D when its destruction was imminent by planting the HM for Dive, convincing Dawn at least that there was no lab on New Clay Ridge, sending them to Kanto to be ambushed by Team Galactic Rocket, and leading them straight to Ghetsis at Laboratory A.
    • You can find a letter written by Ellie to the previous player character that is abruptly cut off foreshadowing that she was kidnapped while writing it.
    • The voice the player character hears in their dream tells them they will find that "things are not always so black and white," foreshadowing the appearance of characters from the Generation V games. The voice also foretells of Dawn's involvement in the story.
  • Freeze-Frame Bonus: In one of the scenes before the villains are revealed and you see only their silhouettes, one of them matches the outline of Bill indicating that Lila has assumed his form.
  • Glass Cannon:
    • Starus and Minusle qualify with their low stats but excellent ability Perfect Match
    • As Legendary Fusions go Zoroxys is fragile but has great Attack and Special Attack stats
  • Good Costume Switch: Archie, Maxie, and Eli have ditched the emblems for Team Aqua, Team Magma, and Team Galactic respectively. Wally has taken off his Team Maqua suit from the first game and went back to his ordinary clothes.
  • Gory Discretion Shot: When the International Police blow up Ghetsis and Lila, Ghetsis is shown badly injured but Lila is just offscreen, horribly mangled having taken the brunt of the explosion.
  • Greater-Scope Villain: Captain Blair's first invasion is the reason modern day Splicen Island is deserted, her manipulating Drayden, Looker, and Hart into bombing it years later is the reason Lila is dead and the once heroic Ghetsis became obsessed with revenge/reviving her, and Blair's death led Ghetsis to take out his anger on trainers triggering the events of the game.
  • Guide Dang It!: While many Fusions can simply be caught in the wild, others are trickier to obtain. For the ones that must be fused with Bill's machine, you'll need to know where to record the Fusion's data in the Pokedex so the machine will recognize it, and also where to get each subspecies which sometimes requires using the Time Capsule or first capturing another Fusion.
    • If you're not the kind of player who uses the Dowsing Machine frequently, you probably won't find the Gracidea Nectar and Shaydile on your own.
  • Guilty Pleasure: Eli insists that he hates "My Lil' Ponyta" but Ellie thinks he enjoys it just as much as she does.
  • Heel–Face Turn:
    • Giovanni after Ghetsis nearly has Lila throw Silver off a cliff.
    • Gijinka Lila after she finds out her life as she knows it is a lie and she isn't really Lila.
  • Hermaphrodite: A new mechanic in the sequel is that fusing a male Pokemon with a female Pokemon will result in an intersex Pokemon Fusion.
  • His Name Is...: Lila tries to tell Ghetsis the name she's chosen for their son, but he can only make out the first letter before she passes. It's N.
  • Homoerotic Subtext: Once enemies, Archie and Maxie have become VERY close in Fusion Generation II.
  • Hostage Situation: Out of desperation following Dialabi's release, Ghetsis decides to use Silver as a hostage to get the protagonists to leave the island.
  • Hot Skitty-on-Wailord Action: You can battle a Trainer with a Wailord and Skitty Fusion who references this trope.
  • Hub Level: Bill's cottage becomes this when he gives it the ability to warp between regions.
  • Humans Are the Real Monsters: Lila explains this to N when he is saddened by Ellie's death. By the end of the game when she finds out what she really is though, she is desperate to become human herself.
  • Humans Through Alien Eyes: Mt. Moon's Clefairy population is so afraid that humans will capture them and turn them into Fusions they flee the planet and return to the Moon.
  • If Only You Knew:
    Lila: I bet he's not even your real father!
  • Impostor Exposing Test: Drayden comes up with a rather drastic one to tell if Bill is really Bill when he suddenly reappears after having been impersonated by Lila, commanding Fragnite to attack him to see if he bleeds.
  • Intergenerational Friendship: Silver and Hart develop one as cellmates in Team Plasma's prison.
  • Interquel: The second Fusion Generation is set between Generation IV and Generation V.
  • Iron Butt Monkey: Eli can't catch a break first getting an entire bike smashed over his head and later violently thrown into a wall, but always ends up okay
    • Lila gets abused even worse, but her resilience is justified since she's not human and it's established that she cannot bleed or die.
  • Irony: When Scientist Arzt finds that all the Fusions in the room have been released, he immediately panics in fear that the player has released Dialabi as well. The player doesn't even know about Dialabi at that point and only ends up finding and releasing it because Arzt then opens up a secret passage and leads them straight to it.
  • It's Up to You: Dawn says this to the player character after she's quickly defeated by Hogia.
  • Jerk with a Heart of Jerk: Although his backstory shows that Ghetsis was at one point capable of doing good things and cared for other people, the Laboratory X flashback shows that he was always a self-centered Jerkass at his core. He was prepared to abandon the island for his family and when the lab is bombed and he is too preoccupied with his own injuries to check on his wife and their unborn son at first.
  • Just Toying with Them: Lila insists she was doing this after you defeat her, claiming her power is actually limitless.
  • Lampshade Hanging: Dawn is the one who likes to point out the absurdities in this game, especially where Team Rocket is concerned.
  • Last-Name Basis: Ellie is the only one who calls Eli Gray by his first name. Even the text boxes use his last name to avoid confusing the two of them.
  • Lightning Bruiser:
    • Milogon, a fusion of Milotic and Flygon you battle in Victory Road, has all around excellent stats but you'll have to work for it if you want one. It can't be found in the wild so you have to make your own with Bill's fusion machine.
    • Hydraqueen is another. Its base form Deinoran can be caught in the wild but it's rare just like the Moon Stone you'll need to evolve it to its final stage.
  • Loads and Loads of Characters: You'll realize at Laboratory X just how huge the cast is when you, Dawn, Silver, Bill, Cynthia, Ellie, Eli, Ima, Jessie, James, Meowth, Drayden, Looker, Hart, Ghetsis, Lila, N, and Zinzolin all assemble in the same room.
  • Long-Lost Relative: Hart turns out to be the player character's long lost father.
  • Meaningful Name:
    • Hart is a play on heart, as in HeartGold.
    • Alma is Spanish for soul, as in SoulSilver.
    • Lila has a lilac color scheme hinting at her relation to Ditto and more significantly Lila's existence is a lie.
    • Gray is what you get when you combine Black and White and the title of the rumored third version of the Black and White games that never materialized.
      • Additionally being a bounty hunter Gray operates in a morally gray area, initially opposing both the good guys and the bad guys and looking out only for himself.
      • His first name Eli is a masculinized version of Ellie. This is because he was conceived as an Expy for Ellie before it was decided that she would return in the sequel.
    • The game's version of history makes N's name one. In the flashback to Ghetsis losing his true wife and son, she dies just before she can finish telling Ghetsis the name she chose for him. Much to his distress, Ghetsis will only ever know that his son's name started with N.
    • When you fuse Staryu and Starmie you get Starus.
  • Merger of Souls: Lila finds this aspect of Pokemon Fusion to be a beautiful thing.
  • Mix-and-Match Critters
  • Mole in Charge: By assuming Bill's identity, Lila very quickly gains control of the protagonists' entire venture. She tries very hard to sabotage their exploration of the island with mixed results.
  • Mood Whiplash: On your way back from your fun shopping trip with Dawn you discover a dead body.
  • Mr Fan Service: Buff, shirtless, scruffy prisoner Hart.
  • Multiple-Choice Past: The memory link feature changes many aspects of flashbacks and battles that you have in the present by reading your Pokemon Fusion Generation save data.
  • Musical Spoiler: Though it's not revealed who the voice talking to Silver in the Forbidden Jungle belongs to until later, the music is a pretty big clue. It's N's theme.
  • Never Say "Die": Mostly played straight when Ghetsis plots to blow up the player in Laboratory D, but averted many other times.
    • Lila very bluntly threatens to kill Silver when he tries to escape.
    • Lila nicknames Ellie "dead girl" after her supposed death earlier in the story.
    • Jessie and James use the word after discovering the body of the real Lila.
    • Also averted when Hart, Looker, and Drayden confess to killing an innocent person in the past.
  • Nightmare Fuel: Arigarig, Baticate
    • Many of the dex entries for fusions are pretty messed up.
  • No Name Given: Though Ellie and Mira's mother was known simply as "Mama" in the first game, this is averted in the sequel. She's given the name Ima as she plays a bigger role in this story.
  • Non-Human Sidekick: Meowth for Jessie and James, Clayzong for Eli, and Swaggy (Becky) for Ellie.
  • Numbered Sequels
  • Official Couple: The E-Team makes it official during the epilogue.
  • Official Fan-Submitted Content: The original 104 Fusions were all made by the developer, but many of the Fusions in the sequel were submitted by fans allowing for many more to be included and obtained in the game.
  • Oh, Crap!: Team Rocket when they see Cynthia again on Splicen Island, and just before they get sent blasting off again in Ever Grande City.
  • Old Save Bonus: Using the Time Capsule feature to transfer Pokemon from your previous game will give you access to many more than you can capture in Fusion Generation II alone.
  • Out-of-Genre Experience: The game suddenly turns into a murder mystery that you have to investigate when you apparently find a dead body in Opelucid City.
  • Overly Long Gag: There's quite a long silence after Team Rocket does their motto at the Hoenn League. Eventually they confess they don't know how to banter with Silent Protagonists.
  • Palette Swap: Unlike the first game, all 440 Fusions have Shiny versions.
  • Parody Names: Shows that are mentioned when you watch TV include Orderly Law RBY, Peck Sent Me to the ER, and Honey Boo-Boos: When Vespiquen Attack to name a few.
  • Post-Final Boss: Gijinka 000.
  • Post-End Game Content: Dawn and Cynthia invite you to the Conference of Champions right after you beat the main game, giving you access to the Kalos region where it's being held.
  • Posthumous Character: Captain Blair of the International Police. It's said that her death before the events of the game is what set off Ghetsis to take out his vengeance on trainers around the world.
  • Previous Player-Character Cameo: Both player characters from RSE, HGSS, and DPPt appear, as well as Red, Kris from Crystal, and Hilda from BW.
  • Punny Name: Ludicrust is a Fusion with one.
  • Recurring Boss: Team Rocket and their boss Giovanni.
  • Red Herring: A masked man stalking the protagonists leaves the player guessing who it could be. It's implied to be the protagonist from the previous game but when the mask comes off, it's...a new original character.
  • Regional Redecoration: A book about Splicen Island claims it was formed when two islands collided.
  • Remember the New Guy?: Ethan appears in Pokemon Fusion Generation, but not Lyra. However if Lyra is chosen as the player character in Fusion Generation II she will take Ethan's place in flashbacks to the first game.
  • Replacement Goldfish: Ghetsis used Alma as a temporary replacement for his departed Lila, and N as a replacement for his deceased biological son.
  • Revenge: A central theme of Fusion Generation II is revenge and how it corrupts people.
    • Ghetsis seeks revenge for his lost love.
    • When Giovanni becomes a fugitive after the first battle with him, he can't wait to pay back the player character.
    • After Giovanni's arrest Team Rocket is motivated to get revenge on Team Plasma for turning on him.
    • When deciding who she wants to battle, Lila considers that she would like revenge on Silver and his Fusion who have attacked her twice, but ultimately decides on the player.
  • Right for the Wrong Reasons: After fleeing Cherrygrove City, Bill shares his hypothesis about what's going on. He correctly deduces that Splicen Island's residents are responsible for hacking his storage system and that they possess Fusions, but his conjecture about their motivations misses the mark and he badly overestimates himself as a central figure in the plot. In reality the conspiracy is much, much bigger than him. Discrediting Bill like he guessed was not one of their primary goals and they had little need for his research as the Fusions had already existed on the island for centuries or more before Bill started creating them.
  • Sanity Slippage: Lila experiences this as the game progresses and by the end is thirsty for blood and begs Ghetsis to let her slaughter all the protags.
  • Seeks Another's Resurrection: Ghetsis has been trying to revive his One True Love. His first test run was successfully fusing living Pokemon with dead ones, and his second was to be trying it out on a human, Ellie's sister Mira.
  • Sequence Breaking: The process of separating a fusion can be exploited to duplicate items. Doing so with a Bicycle Part will let you skip most of Kanto, get the final bike upgrade early, and proceed to Blackthorn City before getting the badge from Viridian.
  • Shadow Archetype: The relationship between N and Silver plays off this. N, whose father manipulates him into helping with his evil plans, is what Silver would be like if his abandonment hadn't lead him to distrust Giovanni.
  • Ship Tease:
    • Eli questions whether Brendan/May was Ellie's boyfriend/girlfriend after she mistakes Eli for them causing her to get flustered and insist they're just a friend.
    • The possibility that there's something going on between Elm and your Mom is played with. In the end she reunites with your Dad.
  • Shipper on Deck: Dawn becomes this for the E-Team by the end of the game.
  • Shoo the Dog: Silver reverts to his cruel, uncaring persona for a moment in Laboratory A when he tells his Fusion to get lost, but it's only an act to get it to leave and save itself because it's so attached to Silver.
  • Shout-Out: A red-haired ghost maid shows up in Old Chateau. She even looks younger for male player characters and older for females.
    • Another AHS reference from Team Rocket "Surprise twirp! I bet you thought you'd seen the last of us."
    • Many shout outs to Lost given the setting of the game.
      • The scientist you fight in Laboratory B is named Arzt.
      • Then when you leave the lab, Ghetsis confronts the protagonists and tells them, "This is my island."
    • The NPC in the Pewter Museum referring to civilizations worshipping fossils is a shout out to Twitch Plays Pokémon and Lord Helix.
    • Pretty much everything Jessie and James do, like dressing up in matching bikinis, is a nod to the anime.
    • Clefairy stealing people's things (in this case Bicycle Parts) to build a spaceship is an homage to an episode of the Pokemon anime.
    • In Dragon's Den there is a shout-out to Cracked referencing a popular article featuring Fusion Generation. The Master echoes the writer's description of Pokemon Fusions.
    Master: It's an abomination! Twisted hellspawn that spit in the face of—
  • Signature Move: Zapmolcuno gets two, Big Bang and Fusion Freeze.
  • Sixth Ranger: Cynthia for the good guys, Zinzolin for the bad guys.
  • Start of Darkness: The game gives a backstory detailing the rise of Ghetsis, the villain from Generation V.
  • Teleportation: The primary means of travel in the game is Bill's teleporting cottage.
  • That Liar Lies:
    Lila: N, you have to understand it was all a lie. This man doesn't care about anyone but himself.
  • That One Level: Players tend to have trouble completing Laboratory C without a guide because like a few of the labs it was not completely finished.
  • The Atoner: Hart set off for the island and left behind his family hoping to atone for what the International Police did years earlier. Eventually Drayden and Looker too decide that they must atone for their crimes.
    • Alma joins forces with Bill to atone for everything she did as Lila.
  • The Computer Is a Lying Bastard: The gym guy in Eterna City tells you flying types are a safe choice to use against Gardenia which is problematic because she leads with an Ice-type Fusion.
  • The Computer Shall Taunt You:
    Lila: Making your Pokemon do all the work? How pathetic.
  • This Cannot Be!: Giovanni and Ghetsis are very confident that their secret weapons, Hogia and Zekresh respectively, are unbeatable so each is in disbelief when they're taken down.
  • This Is the Final Battle: After conquering Laboratory A, Dawn gives you a heads up that the next mission on Splicen Island will be the final showdown.
  • Took a Level in Kindness: Silver, though he's justifiably not very nice to his dad and Team Rocket.
  • Ultimate Life Form: Gijinka 000 describes themself as this.
  • Wham Line:
    Hart: Don't you get it? This isn't Bill.
  • What Could Have Been: A third Fusion Generation game was planned with Hilda as the main character, but canceled due to legal threats from Nintendo of America.
  • What Happened to the Mouse?: Dawn mentions to the player that their Pokemon must be somewhere else as she can't find them among the recovered Fusions, implying that Lugia was not the only Pokemon of yours stolen. However it is the only one you can get back, and this line is never expanded upon.
  • With Great Power Comes Great Insanity: The result of Lila being given her Gijinka powers.
  • Worrying for the Wrong Reason: Dawn is very concerned when Team Rocket goes blasting off for the first time because it defies the laws of physics. Bill reminds her the real concern is that those three couldn't possibly have coordinated the thefts by themselves, so there must be much more sophisticated villains awaiting them.
  • Worthy Opponent: Giovanni, Lila, and Ghetsis all express respect for the player character's skills despite how much they hate the player for all the trouble they've caused.
  • Would Hurt a Child: Ghetsis threatens to blow up the player character just like Team Aqua and Team Magma in the first game.
    • He and Lila are also dead serious about throwing Silver off a cliff if they don't get their way too.
  • You Gotta Have Blue Hair: Dr. Kaseki is distinguished from the other scientists on Splicen Island by this.
  • Your Princess Is in Another Castle!: Dawn thinks that Silver who disappeared may be in Laboratory C, but instead they find his kidnapper who doesn't reveal where Silver is being held. They have to go to several more labs before he reappears.
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