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Clash of the Elements is an adventure/fantasy genre Super Mario Bros. fanfic by mewmaster93. It was started on November 9th, 2011 with Part 1: A Flame Reborn, which was finished on April 2nd, 2012 with the uploading of the Extra Chapter (Though the author has stated that he will update the page again later with a What If? story, which he did after Part 2 ended.). Movie 1 was started on April 6th of the same year and finished on the 24th of that very month. Part 2 was started on the 26th and has ended as of July 3rd. Part 3 has been going on since August 7th, 2012 and ended on November 25. As of January 21st, 2013 Part 4 has begun, and now the fic falls under the Sonic the Hedgehog, The Legend of Zelda and Metroid category for fics due to the changes in locations for Part 4.The story of Part 1 follows Mario as he hears from Professor E. Gadd about the legacy of the Elemental Overlord, a being who quite obviously was able to control all the elements. The legends spoke of how the Overlord had to seal his powers away, and that a new heir needed to be found in order to inherit his powers, since the time was approaching of the day prophecy. Using the Professor's new device to head to the planet Earth, Mario comes across the boy of prophecy, an 11-Year Old named Alex Whiter, who joins him on a journey across the Mushroom Kingdom to find the seven Elemental Stones needed to awaken the Elemental Overlord's powers.Part 1 can be found here (What-If), Movie 1 can be found here (What-If), Part 2 here (What-If for main Part and Gemini's Origin Story), Part 3 here and Part 4 starts here, with the first story seen here The Ocarina of Time and the second one here Desolate Corruption. A story based on one of the main character's pasts can be found here: (Recollections of a Former Goomba) It is highly suggested by the author that you start from Part 1 and don't jump in to the later parts, but the links are there just for the sake of this description.Page in need of some Wiki Magic
Tabuu subverts this, though, because he wasn't a villain.
All There in the Manual: A few things are brought up in the Author Notes and afterthought posts that confirm details not explicitly mentioned in the story itself, such as the fact that Mr. Reality is the one who brought Mewmaster to Plit by complete accident and the truth about the connection between Luigi and Dimentio
Alternate Universe: As a general rule of thumb, all of the What-If stories will take place in one of these, and they are usually brought about via an alternate decision made by someone from the main story. The exception thus far is Part 2's what-if, which was created via the higher-ups so there would be a single timeline where Alex Whiter would find a happy ending.
And I Must Scream: Cackletta's final fate, in which her 'Second Life' spell in combination with Alpha's nanomachines will leave her in a perpetual state of life and death until the spell runs out.
Another Dimension: The Realm of Darkness, Dimentio's world, Smithy's Factory, Final Destination, and the battleground where Mewmaster was sent to fight Smithy and Dimentio
Arm Cannon: Alpha has the ability to create one of these from both of his robotic arms. The primary function of them seems to be to shoot ionic energy in the form of a concentrated laser beam, but only time will tell if they are capable of shooting more.
Apocalypse How: After taking control of Joe Dark's body, the Dark King set in motion events that would bring about a Class 5 to Plit.
Later on, at the peak of his Villainous Breakdown, Joe Dark starts charging up an attack that was stated by the Star Spirits to be capable of causing a Class X variation.
As revealed in Part 2, A Class X-2 Apocalypse happened long ago when the Realm of Darkness started to overtake the real universe, taking many planets and stars into itself before it was stopped.
Tragically, Plit is the first to fall victim to what appears to be a Class Z at the end of Chapter 42 of Part 3. Even worse, this spreads out across the entire universe until only nine beings are left alive.
Apocalyptic Log: There is one in Part 2 that details the final moments of the crew of the Deep Space world before the Heartless devoured their hearts. It is found by Alpha and Mario, and it is implied that this isn't the first time Alpha had viewed it either.
Badass Normal: Captain Florence screams this trope, especially as revealed in Part 3. When Mr. Reality attacked the M.S.I. Base, he drew out Alpha and Gemini's "Shadows" and sent them to fight Florence as he tried to escape the base before the 'Midnight Channel' took it over completely. Not only does he successfully escape, he also manages to beat Alpha and Gemini with nothing but weapons and quick thinking, but he also scars Mr. Reality HIMSELF, all the while keeping his psyche together until he gets far away from the M.S.I. base. Dude has got some SERIOUS balls for a Yoshi.
The Bad Guy Wins: How the Ocarina of Time story ends, when Demise in Ganondorf's body successfully kills Link and causes Riku to go into a Heroic BSOD that makes him abandon Hyrule.
Chaos Alex goes completely berserk after Alex insults his mother's (Cackletta's) name one too many times.
Beware the Nice Ones: Driad. The outer guardian of the Frozen Palace learned this the hard way when Driad regained his memories of his life as an outer guardian and briefly returned to that form to combat him.
BFS: Smithy, especially when he is his human self.
Big Bad: This trope is Zig-Zagged a few times. At first Cackletta looks to be the main villain, but then Joe Dark takes over after Alex defeats her. Then this looks to be switched AGAIN in a case of Hijacked by Ganon and Demonic Possession via the Dark King only for Joe Dark to regain control, but then it is revealed in the epilogue that Cackletta is not only alive, but is working with Dimentio and Smithy, setting up possibly a Big Bad Ensemble, but then as it is revealed in Part 2, noth of them were Cackletta's pawns, meaning that she is the true Big Bad of Parts 1 and 2 all along.
Ganondorf in the first story of Part 4, naturally.
Big Brother Is Watching: Alpha via his Command Sphere, which he uses to monitor every square inch of Plit for the purpose of seeing the heroes' journey and keeping an eye on Cackletta until he joins the group himself.
Big Damn Heroes: Gemini, Geno, and Alpha pull off one of these moments in the very chapters that they end up joining the group in, saving the heroes from the outer guardian of the Lightning Palace, Joe Dark and The Dark Crystal King respectively.
Rosalina does this as well in Chapter 46, saving Mario from dying at the hands of Joe Dark
In return, Mario does this for Alex in Chapter 54 by stopping and destroying Joe Dark's sword from killing him in one-blow
Bittersweet Ending: The end of Part 1. Though Alex has become the Elemental Overlord and stopped Joe Dark, the Genesis Samurais are dead and the Inner Guardians' spirits will never be given the freedom Alex wanted to let them have after taking their souls into their bodies. Because of the Star Spirit's interference during the battle Geno has to stay in Star Haven to mediate the world below.
That's not even getting into the fact that Cackletta is STILL ALIVE, AND SO ARE DIMENTIO AND SMITHY
Bloodless Carnage: AVERTED beyond all belief. Joe Dark's slaughtering of the Genesis Samurai, especially his killing of Cecilia Frost, is bloody to such a point that it is almost nauseating to think about
Boobsof Steel: Cecilia Frost is the strongest female member of the Genesis Samurais and is also the most-endowed.
Book Ends: Alex Whiter's journey in Part 1 begins as it ends, traveling through the Stargadd portal to reach Plit.
Boss Subtitles: In a use of this trope not related to video games, the author uses titles for both the Inner and Outer Guardian fights in the story. He also uses them again in Movie 1 whenever The stronger members of the Subspace Army appear.
Fittingly, considering the origin of this trope, [[The Legend of Zelda: Ocarina of Time}} Ganondorf's]] subtitle is used as the Chapter 2 title in Part 4, and the bosses afterwards also get the same treatment for their fight chapters.
However, in a surprising twist of things, her creation, Chaos Alex proves to be much more successful in his last moments, delivering a speech so powerful to Alex Whiter that it may have been one of the factors involved in his decision to kill himself as he took his evil half down for good.
Breather Episode: The battle against the Lightning Djinn is noticeably less tense in comparison to the other guardian battles before and after it, though this is because the "battle" is actually a simple, friendly game of chess instead of a physical brawl. Though the threat of death still exists for the heroes.
Brought Down to Normal: Happens to Mewmaster and by extension Alex Whiter at the start of Part 3. Most of that part is actually spent trying to regain all of his Elemental Powers as he takes part in Mr. Reality's Game.
Calling Your Attacks: Generally averted for the most part, but there are a few notable examples of this trope appearing in the fic:
"BLAZING OVERLORD FIST"note Spoken by Alex Whiter in the penultimate chapter of Part 1
Cerebus Syndrome: Part 1 starts out with a little bit of humor and some light-heartedness you'd come to expect from a Mario game, but as time goes on and more details get revealed, everything starts becoming rather grim, culminating in the final battle where everything goes to hell and when things are resolved it is a rather Bittersweet conclusion...
Character Alignment: Discussed by Cackletta in Part 2, who cites it as one of the reasons why no one in the universe is worth keeping alive.
Chekhov's Gun: The broken text from the tablet last mentioned in Part 1, which is connected to another Chekhov's Gun that Alpha acquired in the "Remembrances of Alex Whiter" side story. Both of these guns are fired come Part 3.
The Device Alpha used to breech the Realm of Darkness in Part 2 is used again in Chapter 35 of Part 3.
Chekhov's Gunman: From the dialogue said at the end of Part 1's Extra Chapter, the lady in the robe has set herself to be one of these, but only time will tell when she shows up again.
Remember the outer guardian of the Lightning Palace? You know, the giant Koopa with the muscles and an arrogance issue? Yeah, he's actually Commander Zeta's brother, inflicted by the outer guardian curse.
The Chosen One: Alex Whiter is the one foretold in the prophecy to become the next Elemental Overlord. However, Alex points out to Mario how improbable it is that he fits the role so perfectly.
Crazy-Prepared: Alpha is a deconstruction of this trope. He is so prepared for every possible scenario, including the possibility that everyone he knows on the planet could one day become corrupted or be forced to reveal information to the enemy that he has been consumed by a feeling of paranoia that has left him unable to trust let alone form a bond with the people that stick around him, save for Mario that is.
Commander Zeta explicitly notes that he created his hyperspace pockets just so he could be prepared for every possible scenario.
Crossover: As of Chapter 22 of Part 2, with the Kingdom Hearts universe.
There is also one with Persona 4, which seems to be the center of the plot in Part 3.
Curb-Stomp Battle: Chief Chilly is defeated in the span of 2 paragraphs in Chapter 23 of Part 3, not even getting to use any attack beside a basic charge. Also counts as an Anticlimax Boss in comparison to the other new outer guardians. Both examples are lampshaded by Mewmaster.
Dangerous Forbidden Technique: The Blazing Overlord Fist, which causes an excruciating amount of pain to the user that lasts seemingly forever unless they get protection from it which E. Gadd so kindly supplied for Alex, and after dealing with the pain it is mentioned that unless the energy is released every now and then an ensuing build-up can increase the power of the fist to the point that it can destroy worlds if unleashed...
Darker and Edgier: Part 2. There is little to no humor, some rather grim scenarios are brought up during Smithy and Dimentio's (Fake) backstories, including Betrayal, paranoia and the strong pursuit of a dream leading to the death of Smithy's closest friend, Dimentio casually mocking the love of Blumiere and Lady Timpani, along with his fabricated story that mentioned a pregnant Daisy DYING during an alien invasion. And that's not even getting into Chapters 21-29...
Dark and Troubled Past: Alex Whiter had one of these, which he purposely kept secret as revealed by the Chronicler (Who was actually Alex pretending to be the Chronicler)
Joe Dark had one of these as well.
Darkest Hour: The end of Chapter 49 of Part 1. All the heroes are down for the count, Rosalina has fallen after proving unable to deal with Joe Dark after he went into his Griffon Form, the Genesis Samurais are all dead, the Dark King managed to set up a widespread spread of destruction across the planet during his brief moment of possession, Alex Whiter has had his subconsciousness destroyed, and Joe Dark is ready to destroy the Origin Temple, unaware that his attack will actually annihilate the rest of the planet too...
Deadpan Snarker: Alex and Gemini both have their moments throughout Part 1.
Deal with the Devil: Joe Dark forges a pact with the Dark King's spirit so he can have the capability to destroy Alex Whiter.
Death Equals Redemption: Smithy, who dies realizing that he managed to create a living weapon in the form of Gemini who has actually managed to overcome the desire to destroy lingering in his demonic heart and has become a force of good that he can be proud of before he finally falls into eternal slumber.
Death Glare: All of the heroes give this to Joe Dark after he finished killing all of the Genesis Samurais
Defeat Means Friendship: Most the heroes manage to form a bond of friendship with their respective Genesis Samurai opponents, save for Geno, who was already acquainted with them long ago, and Luigi, who was knocked unconscious after his battle before he could form one with his.
Demonic Possession: Mr. Reality by the invisible, subconscious burying parasites called the Parakali
Demoted to Extra: Pretty all of the main cast from the first two parts get little to no screentime during Part 3. Justified though by the fact that the story is done with a first-person narrative focused on Mewmaster, so the scene can't really change to focus on them or what they are doing.
Designated Hero: Brought up In-Universe by Joe Dark, who claims that Alex Whiter is getting undeserved treatment as a good guy after some sort of atrocities he committed in the past.
Despair Event Horizon: According to Joe Dark's backstory, he went through this when everyone alive in his family tree was slaughtered by some unknown person/force
A combination of Daisy's death (along with the child she was pregnant with), an inability to conquer his inferiority complex, and the cold realization that he had slaughtered all of his friends along with his brother led to an alternate future version of Luigi becoming DIMENTIO
Downer Ending: Part 2, which ends suddenly with the revelation that Alex Whiter sacrificed himself to destroy his evil counterpart.
Dropped a Bridge on Him: All of the Genesis Samurais qualify for this trope, but in particular is Pitori Sparks, who was given an offer by Gemini to join the M.S.I. before his life was cut short
Dying Momentof Awesome: Even though Zeno Blaze is the last to die against Joe Dark, he goes out not only performing a Shut Up, Hannibal! to him, but summoning a large pillar of flame against him even though he knew it wouldn't harm him.
Alex Whiter's Heroic Sacrifice against Chaos Alex
Eldritch Abomination: Pandora, the dragon trapped within Subspace, who is said to be able to drag a world into Subspace if it were to ever fully emerge from a Subspace Orb. It is also stated to have a rather netherworldly glow around it...
The Leviathan, Shattered Reality.
Elemental Powers: The Elemental Overlord had control over a wide variety of these. Over the course of the story the heroes come across temples based on these such as Nature, Water, Wind, Lightning, Earth, Ice, and Fire. By the end of Part 1, Alex Whiter has gained the ability to use these powers as well.
Foregone Conclusion: No matter how hopeful things look in Recollections of a Former Goomba... Commander Zeta is going to be killed by Cackletta, Alpha will lose an eye and the two of them more than likely won't collect all seven Elemental Stones, the last of which has already been mentioned in-story by the Drill Golem Onyx
Foreshadowing: Hints of future plot events are thrown out quite often in Part 1 alone. A few examples include:
Rosalina'sBig Damn Heroes moment, were it not easy enough to figure out before, had the clearest hint given at the end of Chapter 35 with the words: "shadow of an observatory"
Likewise, Mario destroying Joe Dark's sword with his star energy is hinted at during previous battles against him, where star energy was proven to be capable of dealing critical damage to beings consumed by darkness.
This hint is a bit of a stretch towards the end result, but The Genesis Samurais' souls going into Alex's body was more than likely foreshadowed by this line:
"Though his body may be weak, his soul still lives. And as long as that's alive, then he shall live as well"
Gambit Roulette: As Cackletta revealed, everything her allies, the heroes and herself had done over the course of two-thousand years was all part of a two-sided plan to either get her the Elemental Overlords powers or give her the resources needed to create a new Dark King.
Gem-Encrusted: The walls of the chamber that holds the Terra Cave's Elemental Stone.
Giant Mook: The outer guardian of the Lightning Palace is already bigger than the average Koopa, but he is able to take this trope Up to Eleven by using the metal straps on his body to turn his body into a lightning rod and increase his size even further via the electricity that is drawn to him.
Hoist by His Own Petard: However, it is because of that very ability that Gemini is able to ultimately kill him, by overloading him with electricity to the point that his heart suffers from too much strain and shuts down.
Good All Along: Gemini discusses this trope with Mallow in Part 2, more specifically referring to Domino when he does so.
Godzilla Threshold: The threat of the Dark King's return is so great that the Star Spirits are implied to reluctantly be willing to lift a [[spoiler: ban just so Rosalina can combat him if the need arises.
Great Offscreen War: The war between the Elemental Overlord and the Dark King's forces that caused the series to happen in the first place.
The Heartless: The trope namers themselves have appeared as of Chapter 22 of Part 2
Heroic Sacrifice: Driad REALLY doesn't like the implementation of this trope, and the one deciding factor that made him dislike it is when The Genesis Samurais sacrificed their mortal bodies against Joe Dark
And that is honestly going to be a bad thing considering Alex Whiter sacrificed himself to stop his evil counterpart
In Part 2, All of Smithy's creations minus Axem Red, Smithy himself, Dimentio, Cackletta, Chaos Alex, and Alex Whiter
In the What-Ifs, Not counting the millions of people that are erased in the cataclysmic events that unfold we got Alex Whiter and Joe Dark/Dark King in Demise Under the Stars, Alex Whiter, Tabuu and Cackletta in Return to a Blank Slate, Chaos Alex in Confusion from Chaos and Koopis in The Unrelenting Beast
The Master as of Chapter 22 of Part 3.
The Dark King's spirit has been permanently expunged from the mortal plane by 'D.' as of the prologue of Part 4.
Though Foregone Conclusion is in effect for this, it doesn't change the fact that Commander Zeta, Mario and Luigi's parents and Bowser's father Balroc are all confirmed dead via Recollections of a Former Goomba.
Made of Iron: Alex Whiter has a ridiculous record of getting hit with attacks that would kill any normal human, which is a bit crazy considering that in spite of his flight he only has an above-average level of strength. When one takes into considering his Determinator status...
The Man Behind the Man: Part 2 reveals that Cackletta is responsible for all the villainous threats to Plit beforehand, up to an including Joe Dark and Tabuu
Mind Screw: Besides the Big Lipped Alligator Moment entry entry in the YMMV section, there is also the aftermath of Cackletta's defeat in Chapter 42, which was actually done on purpose by her to mess with Alex's head.
Mr. Exposition: Alpha, and Geno when it comes to matter related to the Star Spirits
My God, What Have I Done?: Immediately after Mew frees Mr. Reality from the control of the Parakali parasite, Mr. Reality realizes just how badly his powers have screwed things up especially after witnessing the blank expanse that was brought on by the near erasure of reality.
Mythology Gag: Luigi being a Queen in the chess game against the Lightning Djinn actually offers a two-fer on this one. Not only is it a reference to the time he had to wear Peach's dress in Mario And Luigi Super Star Saga, but it also references an obscure Mario chess game where Luigi is the Queen piece, which can be seen here 
Not Quite Dead: Cackletta TWICE!, Fawful, Smithy and Dimentio. The return of the third guy is brought up and Lampshaded by Mallow to Mario in Chapter 3 of Part 2:
"Do you go easy on them or something, or do you keep forgetting to check and make sure that you weren’t fighting copies of their true selves?"
Alex Whiter, as it turns out.
No Sell: Joe Dark does this to Everything the Genesis Samurais toss at him.
Omniscient Council of Vagueness: The "Higher-ups", three beings who watch over the multiverse Save for the Realm of Darkness, as revealed by Cackletta and govern it towards an unknown purpose.
One-Winged Angel: Bowser becoming Giga Bowser An interesting variation of this trope because in this case It was not an intentional transformation
Joe Dark's Griffon Form
Averted in Smithy's case, for instead of going with the form he used in the original game he merely sheds his armor and reveals his human body. Though it still proves deadly enough once he starts fighting.
Outof Focus: This happens a few times in Part 1 to some of the heroes once the group gets big enough, but the most obvious example of this trope is Mallow, who save for Mario really doesn't get a character arc devoted to him throughout the story. He is also the only one whose fight is not given any attention to in Movie 1.
However, this is subverted in Part 2, where not only does he share plenty of screentime with Gemini during the Smithy arc, but it is because of him that Gemini Doesn't eventually lose himself to his demonic heart
Pet the Dog: According to Smithy's recollection of his childhood, the Dark King commended his craftmanship without any hints of malice in his voice, and it is even stated that the Dark King carried that very sword with him to his death.
Physical God: In Part 3's what-if, Alex Whiter becomes one of these when he enters his Apex Phoenix Form. It says a lot when with just one punch, Alex managed to kill, not briefly stop, Shattered Reality.
Pillar of Light: Shows up every time the heroes transform in their Star Spirit forms. Also happens in Chapter 50 when Alex's health is being restored by the Star Rod
This trope generally tends to be Geno's mode of transportation between Star Haven and Plit, though his pillar has a more starry design to it.
Posthumous Character: The Elemental Overlord and the Dark King. Though this is a weird case of this trope, since though their physical bodies are dead their spirits still reside within their new successors. However, in the case of the Dark King, we learn more about him through his suboordinates, especially in Smithy and Cackletta's flashbacks.
Also, Former M.S.I. Commander Zeta, who was killed thirty years ago and the act of avenging him forms the basis of Alpha's motivations.
Power Gives You Wings: Alpha and Gemini's Star Spirit forms grant them angelic wings, though they aren't actually used for flight and Alex Whiter's Phoenix Form, which gives him the creature's majestic wings
Sequel Hook: In the Epilogue of Part 1, where The two mysterious beings who were watching the battle between the heroes and Joe Dark are revealed to be Dimentio and Smithy, and Cackletta is revealed to be alive, showing that she acquired one of the feathers from Alex Whiter's Phoenix Form for some evil purpose...
This also happens in Movie 1, with Alex promising Tabuu that he will avenge his people by finding and killing The Master Hand
Seven Deadly Sins: According to Cackletta, The Dark King's control over darkness stemmed from a balance between all seven of them, and that his death was caused because he succumbed to a few of them simultaneously.
Each Sin Samurai inside of Chaos Alex embodies a different one of these sins.
Ship Tease: Tina Aqua with Alex Whiter in Chapter 35 of Part 2
Shout-Out: To Super Mario Bros. Z in Chapter 45 More specifically, the act of having the Star Spirits appear and using their energy to power-up Mario and the other heroes, a concept which, while it didn't get to appear in the actual series, at least got shown in the intro. Thankfully, the author gives Alvin-Earthworm full credit for the idea instead of claiming it as his own.
Another example of this trope with the same series happens in Part 2, where The Axem Rangers X, with descriptions of their designs matching the sprites Alvin used appear in the early chapters.
The battles against Shadow Gemini and False Shadow Geno fittingly play out like battles from Persona 4, and save for damage outputs the details are pretty accurate towards the series itself.
Shut Up, Hannibal!: For every speech that Cackletta tries to give to break the heroes' resolve, each one of them has a counter to it. The best example of this comes from the response to Alpha'sBreaking Speech, in which both himself AND Mario break each and every one of her points down and give her a Breaking Speech of their own towards her.
Spanner in the Works: Fawful, Alpha and Mario to Cackletta's plans. And Bowser too, for freeing the Star Spirits from their imprisonment. The later case is lampshaded by the author in his final thoughts on Part 2
Take Our Word for It: Parodied during the Terra Cave portion of Part 1, where Gemini and Alex come out of their tunnel bragging about how awesome it was to traverse it and they tell the remaining heroes that they should've been there to see it.
Talking Is a Free Action: Subverted like wildfire throughout the story, where the heroes will attack the villains during their monologues or vice versa.
Throwing the Fight: Tabuu does this in the final confrontation with Alex in Movie 1, since he saw no reason to break the boy's determination to win even though he easily could've
Averted in the What-If though, where Tabuu kills Alex instead of listening to him
Time Skip: 1 month between Part 1 and Movie 1, and two months between that and Part 2.
Part 3 takes place one year after the conclusion of Part 2.
Time Skips are all over the place in Part 4 thus far. The first bit of the prologue takes place 3 months after the end of Part 3, the second bit takes place a few months after that, and Riku Mew is created 6 months after that according to the author, making for a grand total of a year having passed between the true start of Part 4 and Part 3.
Time Travel: This happens involuntarily to Alex Whiter in Part 1's Extra Chapter, which sends him two-thousand years into the past. Though the cause is not stated at the moment The mysterious lady from the past mentions about something called the "Gaia Temporis"...
The Only One Allowed to Defeat You: Joe Dark states this firmly to Mario when he first appears, and he has no problem attacking anyone who defends Alex from him. As all the good guys find out in the final battle.
Tomato in the Mirror: Driad is not a Good Guardian, but actually the former Outer Guardian of the Nature Castle
Likewise Alex Whiter does this three times near the end of Part 1. First by getting the Elemental Overlord's powers, then after getting The Elemental Forms from the Genesis Samurais spirits, and finally acquiring the Phoenix Form
Transformation Is a Free Action: The robed lady in Part 1's Extra Chapter makes a point to Alex after their fight that this will not always be allowed in battles, especially against wiser opponents.
Vague Age: Averted for the most part, but there are two notable exceptions:
Gemini, whose age can't really be pinned thanks to the fact that it is impossible to determine how old he was when Smithy kidnapped him from Koopa Village
And then there is Alpha, where the only hint given for him is that he was alive thirty some years ago.
The Unfought: The inner guardians of the Terra Cave, Frozen Palace, and Ignitor Cave. Though their powers are given to the people who merge the Elemental Stones with themselves. This also counts as an example of The Unseen.
Though this is no longer the case with the Terra Cave and Frozen Palace guardians, who are both seen and fought by Alpha and Commander Zeta in the Recollections of a Former Goomba side-story.
Unwitting Pawn: As revealed in the Epilogue for Part 1, Joe Dark, and by extension the spirit of the Dark King was this to Cackletta
Actually, as of Part 2 EVERYONE in Part 1, and in all the Mario Games before that were this to Cackletta. The only exceptions are Fawful, who was The Mole and knew he was being played, Alpha, who was wise enough to see through her tricks, Rosalina, and the Star Spirits
Villainous Breakdown: Joe Dark goes even MORE insane over time in the final battle, but what really breaks him is when Mario breaks his sword.
Villain Episode: The first chapter of Part 4, save for the first few paragraphs introducing Knuckles and Angel Island focuses entirely on the recently revived Joe Dark as he arrives at Sonic's world in order to become stronger via the negative energy of the Chaos Emeralds
Well-Intentioned Extremist: Joe Dark THINKS he is one of these, but as Alex points out to him after learning of his backstory, his ends don't really justify the means.
Tabuu, on the other hand, actually fits the definition of this trope.
From the same Part, Chapter 25 where Cackletta reveals that the Kingdom Hearts universe was in fact consumed by the Realm of Darkness long ago, a process that occurred after Xemnas killed Sora and Riku and absorbed their hearts into his own body.
Then there is Chapter 26, where Cackletta talks about how everything up until this point in time was all part of her plan to acquire the Elemental Overlords powers for herself or create a new Dark King
The Final Chapter of Part 2, in which Alex Whiter killshimself to destroy Chaos Alex once and for all.
The Epilogue of Part 3, in which Joe Dark is brought back to life by the Dark King's spirit and the Dark King reveals that Joe Dark can become stronger by absorbing mass quantities of negative energy. His first target? The seven Chaos Emeralds.
The second chapter of "The Ocarina of Time" story ends with Ganondorf completely wiping the floor with Riku Mew and stealing his darkness to become stronger.
Later on is Chapter 29, which ends with a big deviation from Ocarina of Time's climax Demise is back, and he has possessed Ganondorf's body.
The final chapter and epilogue is an even bigger Wham Episode. Not only does Demise KILL LINK, but Riku is thrown into a Heroic BSOD so strong that he actually abandons Hyrule to its fate...Not only that, but because of Demise's return a series of events unfold that lead to the creation of the DOWNFALL TIMELINE
Chaos Alex qualifies for this as well. On top of being He starts off his "new" life by witnessing his mother/creator die before his eyes, and before he can do anything he is instantly taken over by the Dark Star, and act of which causes a lot of pain before he frees himself. After that he continues to be unaware of how callous his mother truly is as he goes out to fulfill her plans. And this isn't even getting into what happens as he fights his good counterpart...
Worthy Opponent: Albeit with a begrudging attitude towards the admission, Cackletta calls Alpha this after her revival in Part 3