Kirby Super Star: At first, Marx appears to just be another harmless, cutesy resident of Dream Land, but in fact he tricks the sun and moon into fighting, gets Kirby to summon Nova to stop the fight and then uses Nova's power to take over the galaxy. Then, in Kirby Super Star Ultra, he is resurrected from his former defeat in a demonic form by absorbing Nova's power.
Shadow Hearts' Seiji Kato started off as a lovable goof with a kind heart, an eagerness to please, a crush on his superior officer, and next to no knowledge of magic, instead having studied geography. He summoned the ancient gods of Japan in an attempt to completely rewrite history and erase an entire timeline. Because his "girlfriend" died twice on him.
Psaro The Manslayer from Dragon Quest IV, a pretty boy who builds up a hate for humans because cruel men want his elf girlfriend's ruby tears and hurt her for them, He gathers monsters to invade other towns in order to kill the legendary hero/heroine, but is simply rumored by regular people as a random cruel arena fighter. When Psaro's girlfriend, Rose, is actually killed by humans, he goes mad and seek a way to evolve into a monster, and you have to fight him as a final boss.
Let's not forget the Big Good and Big Bad of the series: Marcus Cole was exposed to mustard gas during WWI, and after the war went globe-hopping with his now-mercenary platoon buddies, including his best friend Stephen Richter looking for a way to save his life. They eventually find the Well of the Furies, and drink from the Fountain of Zeus. Not only does this fix Marcus, but these two nobodies, these barely-notable privates in a war fought by millions, are now the first Incarnates of the gods themselves in generations, going by the respective names Statesman and Lord Recluse
Darrin Wade fits here, what with his killing Statesman's daughter and then Statesman himself. Oh, and he also plans to summon Cthulhu Expy Rularuu into this dimension and merge himself with it. Not bad for a rejected mage.
Soul Calibur's Siegfried was the leader of a rag-tag bunch of thieves; not much to write home about. After robbing a convoy where he mistakenly decapitates his own father and quickly loses his mind over it, convincing himself that someone else did it, he takes it upon himself to locate Soul Edge, thinking that his father's murderer deserves no less than death by that blade. He finds it, alright...
In Soul Calibur III Siegfried and Nightmare become separated. So Siegfried is no longer a Nightmare. He's just responsible for unleashing a villain that lacks any semblance of a conscience or humanity whatsoever. Oopsie. Then in Soul Calibur IV in his ending he allows Soul Calibur to bring "peace" to the world by covering it with crystals to trap it in stasis forever.
On the other hand, his father was a brave knight that was seen as a champion of the peasants, and went on a crusade. He arguably wasn't a complete nobody...
In Dark Cloud 2, Sirus was a peaceful, shy Moon Person (anthropomorphic rabbits) who liked flowers, and, after sneaking into the Palace to admire the gardens, was invited by Queen Alexandra to become their keeper. When war broke out over the three Atlamillia Stones, devastating the country and killing Alexandra, he obtained the Sun Atlamillia and swore eternal vengeance upon mankind. Ten thousand years later, the Dark Emperor Griffon has all but destroyed the world by manipulating the timestream, and sending out his armies to devastate the few resistance forces that he hasn't erased from existence.
In the Ace Combat games, your characters always start as unknowns, but quickly become the reason for much Oh Crap from the enemies.
Aldo Trapani, the real player character of The Godfather: The Game, was originally just the son of a Corleone-aligned baker. Ten years after his dad gets gunned down by Barzini goons, though, he gets taken under the wing of Luca Brasi and quickly becomes the top Corleone hatchetman, effectively crushing the other four families and becoming the new Don of NYC. Averted in the sequel, where Dominic is already established as Aldo's underboss prior to the start.
It's mentioned in the Mass Effect lore that The Illusive Man, Visionary Villain and leader of human extremist group Cerberus was once a normal man with a family named Jack Harper.
Also, from the Reapers' perspective, Shepard him/herself. Starts out as a farmer/ordinary soldier/spacer, depending on the player's choice, but becomes the single greatest threat to the Reapers in tens of millions of years.
This is especially prevalent if Shepard becomes a Renegade. The player has the option to portray Shepard as a near-Villain Protagonist and sociopath, willing to do things from ruthlessly killing innocent people for the good of the mission to shooting an adoring fan in the foot.
The Shadow Broker turns out to be a member of a primitive species who was enslaved and trained to be the original Shadow Broker's chief enforcer. He killed the original Shadow Broker and took his place.
Up to a point, the Krogan race. A proud warrior race that was way behind the rest of the galaxy technologically, they were eventually used by the Salarians as soldiers against the Rachni. With exposure to other cultures and better technology, the Krogan became a threat to all other races, to the point the Salarians had to cull their numbers with the Genophage.
The Geth are another example. They started their lives as simple labor devices with the ability to learn, but eventually developed the ability to philosophise. Fearing they'd want their freedom and rebel, their creators decided to wipe them out... only to lose the war so badly, they were driven from their homeworld and forced to become interstellar vagrants. When the Geth finally reappear three centuries later, they're allied with the Reapers and try to take over the galaxy. Although it's later revealed the "True" Geth actually desire peace with their creators and only acted in self-defence. The Geth who have allied with the Reapers are "Heretics" and only represent a small minority.
Subject Zero, AKA Jack, full stop. She could have just been a regular girl, had Cerberus not gotten hold of her. But, because of that, she is the most powerful human Biotic in the galaxy (depending on your beliefs of Adept/Vanguard/Sentinel Shepard's own Biotic skill), on par with Asari Matriarchs.
Shepard's clone started out as a simple source of spare parts during Project Lazarus, and eventually becomes a serious villain with a highly xenophobic agenda.
Throughout the Baldur's Gate series, the Player Character goes from being just some kid with a tiny fragment of the God of Murder in them to a being of incredible power. The bad guys in the third game don't send assassins after you - they send an army. You can also become a God, if you choose.
Sarevok, and most of the rest of the Bhaalspawn that become major forces. Sure, they have a fragment of the God of Murder in them, but lots of people had that, and most of them didn't amount to much of anything. Sarevok, for example, goes from an orphan with a tiny fragment of the God of Murder in him to extremely deadly warrior and a good enough manipulator that he actually is elected Grand Duke of Baldur's Gate.
Neverwinter Nights 2, with its first expansion pack, is maybe an even better example. At the start, protagonist is just another inhabitant of West Harbor, not really remarkable except for the shard. At the end of Mask of the Betrayer he/she can, if you so choose, become a superpowered abomination that devours souls, and is capable of doing that to any number of people at once and even to gods. Cue a Roaring Rampage of Revenge of eating its way across Toril and the Planescape.
For all we know, Gorion's ward could be among the gods that get eaten.
In Dragon Age: Origins, two of the available origins really are nobodies - you can't get more 'nobody' than an elf living in an elf ghetto or a Casteless dwarf. You then go on to command the armies of an entire country, whose combined power is more or less equal to your own. You can even become the first person ever to slay an Archdemon without dying, though you need some "outside help" for that one...
Loghain is a better example; he wasn't even a noble before the Orlesian invasion and ended up as a Teyrn (roughly equivalent to Duke in medieval England), father-in-law to the King, and eventually regent over the land of Ferelden through a combination of clever military tactics, ambition, and backstabbing.
In the Warden's Keep DLC, you read passages from a journal about a young boy being made king because he was thought to be easily manipulated. However, he becomes Drunk with Power and ends up executing entire noble families as punishment for them talking back to him.
In Dragon Age II, Hawke starts out a penniless refugee forced to eke out a living in the slums of Kirkwall. By Act II, s/he is the head of a rich noble estate. By Act III, the Champion of Kirkwall. In one ending, the new Viscount of Kirkwall, in the other, the banner of the mages' rebellion against the Chantry across all of Thedas.
Happens three times in Chzo Mythos the first is John DeFoe by the way of being beaten to death with an enchanted idol then in the prestory Cabadath becoming the Prince, then Theo Dacabe becoming the New Prince.
Arguably, the Boss from Saints Row. At the beginning of the first game, he was just some guy on the street. By the end of the second, though... hoo, boy. Just ask the Stilwater Police Department.
The Boss ends up becoming the President in the fourth game and must fight off an alien invasion. The end of the game sees them as the ruler of said intergalactic alien empire, with access to time travel.
World of Warcraft: Kel'Thuzad, a second rate mage, discredited and harassed by the mages ruling council for a bit too much interest in certain taboo fields of study like necromancy. Takes one little trip to that planet's version of the Arctic, comes back as leader of a death cult, spreading a plague of Undeath through the human kingdoms, bringing most of them to their knees before finally getting killed; only to come Back from the Dead and become The Dragon for one of the most powerful forces of Evil in the World.
Although according to WoWWiki, he was a member of the Kirin Tor's Council Of Six. They might have expelled him from the order, but it doesn't seem as though he was a nobody before that.
Kel'Thuzad was an Archmage of Dalaran and a man of considerable wealth and political standing, as well as being one of the Six. However, it has to be said that simply being an archmage and member of the Council of Six does not make one a noteworthy lore character, since most of its current members are relatively minor NPCs in WotLK. That said, this trope could be said to apply in that he started out as 'just' a powerful and influential mage who dabbled in necromancy (and was terrified by what he saw in Northrend), to being an incredibly powerful necromancer and the second-most powerful undead entity on Azeroth behind the Lich King.
Garrosh Hellscream started off as the pathetic, fatalistic leader of the Mag'har, wrapped up in self-loathing after learning his father was the one who corrupted the Horde. After Thrall showed him how Grom had died freeing the Orcs, Garrosh began to act more like a typical orc warlord: Brash, violent, and a bit short-sighted. He eventually became Warchief of the Horde and then the final enemy in Mists of Pandaria, and is a founding member of the Iron Horde.
Even worse, The Great Will, or YHVH. He was once a God among many, with only a few more followers than the norm. This was enough to allow him to destroy and demonize his opponents, and led to him becoming a Mad God ruling across universes and the ultimate manifestation of the concept of Law.
In Alpha Protocol, one of the options you can start with is as a "Recruit", in which you are, well, a raw recruit with no field experience (and no starting skill points): in other words, a "nobody" who will make for a perfect fall guy if anything goes wrong. In one of the possible endings, you agree to work for the Big Badbut then betray him, having made enough friends in both high and low places to run your own Conspiracy and manipulate world events from the shadows.
There's also Steven Heck, the Crazy AwesomeConspiracy Theorist alleged-CIA Agent who's implied to just be a regular guy who decided out of sheer insanity to be the best Conspiracy Theorist in the world.
Prototype is the embodiment of this trope. The player character starts waking up from death relatively powerless and gradually becomes the scourge of the US Army.
In the plot it happens twice. First, by all accounts innocent college student Elizabeth Greene became an immortal host for the Redlight virus and a OneWomanZombie Apocalypse. Second, poverty-stricken, abused foster child Alexander Mercer grew up to get a degree in genetics, create the deadliest virus in mankind's history and with it attempt to take the whole human race with him when he died. That accidentally made his corpse the immortal host for the Blacklight virus and a Person of Mass Destruction - the player character.
Possible for the Courier in any myriad of ways in Fallout: New Vegas. Starting out as some nameless schmuck with a couple holes in your head, you can go on to be seen as the scourge of any (and all) of the main factions in the game.
Also from New Vegas: Edward Sallow and Joshua Graham. One, a Follower of the Apocalypse with a chip on his shoulder and a fondness for history. The other, a Mormon missionary with fluency in tribal languages. After the two were captured by the Blackfoot tribe, Edward decided to teach them about war, becoming their chieftain, while Joshua served as his interpreter and, soon after, his second-in-command. Therein lies the origin of Caesar, the Malpais Legate, and the Legion.
And now we can add Ulysses to this list, with the release of Lonesome Road and the revelation that he was simply a member of a tribe conquered by Caesar's Legion who eventually rose to become a Fruumentarius, who after an event caused by The Courier came to the realization that one person can shape history. After Walking the Earth a bit and settling down to become a rancher/courier, the revelation that the person responsible for the event was alive and kicking led to the events of Lonesome Road, where he plans to nuke the Mojave in his own attempt to shape history.
As an entire species, Deathclaws are this. Start as harmless chameleons, but become the most terrifying creature on the planet after a little bit of genetic engineering.
Normal Bloatflies are merely annoying bugs, but the Legendary Bloatfly from Old World Blues is one of the most difficult optional boss enemies.
This is seen in Lands of Lore III. While the Big Bads of the previous two games were the sorcerous leader of the Evil Army, and then the setting's Crystal Dragon Satan, the main villain of the 3rd game turns out to be one the series' secondary supporting characters, who starts the game as comic relief and progressively turns villainous as he grows increasingly desperate while his plan to avoid death begins to unravel.
In Portal 2, we find out that Cave Johnson's secretary, Caroline, underwent Brain Uploading on Cave's orders after his death, as he felt Aperture would be in good hands with her. The computer her brain was uploaded into? GLaDOS.
The same trope can also said to have been invoked in Wheatley, who turned from being just one of the many personality cores within the Aperture Laboratories to being in charge of the entire facility...for a while.
Phantasmagoria: A Puzzle Of Flesh definitely uses this trope when the origins of the Hecatomb are finally revealed: it's actually the original Curtis Craig (not the one you've been playing). He started out as an innocent child who just happened to be in the same room as Paul Warner while he was looking for test subjects. Flung into another dimension and forced to watch as he was replaced by an alien duplicate, he plotted revenge; twenty years later, he's developed powerful psychic abilities, and he wants the duplicate's body for his own.
Runescape is a good example too, you start off as a slightly tougher than normal human, who could end up being killed by giant rats, to an unstoppable juggernaut who has slaughtered their way through thousands to millions of enemies, wielding ultimate arcane power, not to mention the ability to summon giant metal beings that are exceedingly tough, with the ability to kill regular citizens with one punch, arrow, spell, with a bank account filled with potions that make you MORE unstoppable, dozens of ancient artifacts, enough regular weapons to outfit a small army, enough ranged weaponry(and the skill to use it) to qualify as a piece of artillery. You also end up being the most important person in the world just because of the aforementioned skills and involvement with...everything.
In Soul Nomad & the World Eaters, Revya starts off as a normal person, living in a hidden village with his/her best friend. Then, his/her soul gets fused with Gig's, and becomes so powerful that he/she destroys two of the World Eaters with ease, takes over the entire kingdom of Orviska and ends up destroying all of reality
In Sonic Adventure, Chaos, the watery humanoid being who grows bigger and stronger by consuming Chaos Emeralds, is called the god of destruction, and is responsible for destroying nearly all of the Echidnas, started off as an ordinary Chao, one of the adorable little critters you can raise in the eponymous gardens, until exposure to the Master Emerald mutated him. Then the Echidna tribe tried to take the Chaos Emeralds for themselves, hurting several Chao in the process. That resulted in Chaosearninghis title.
In DragonFable, humble blacksmith apprentice Konnan turns to fire magic and renames himself Drakonnan after the hero failed to save his family from the fire dragon Akriloth. Drakonnan quickly surpasses his Evil Mentor Xan and Akriloth in terms of sheer evil.
Claude of Grand Theft Auto III goes from being a random mook (his first couple of jobs consist of driving prostitutes around and giving beatings to drug dealers who aren't paying their dues) to a feared and hated hitman who kills pretty much every gang leader in Liberty City.
CJ of Grand Theft Auto: San Andreas goes from being a random gangbanger (not even leader of his own street gang!) to semi-respected businessman and head of a criminal empire that extends over the entire state.
In Ghost Trick, Yomiel goes from being a computer programer (albeit one of the best) to being a disembodied spirit with the ability to possess other people and move his own time-frozen corpse like a puppet.
In most of the Zelda games, Ganondorf was a kid from a poor Gerudo tribe, who went on to become insanely powerful and nearly conquer Hyrule. In The Legend of Zelda: Majora's Mask, we also find out that the Skull Kid was...well, a kid who liked to joke around, and ended up possessed by an evil mask, summoning a giant moon to the ground. The Legend of Zelda: The Minish Cap has Vaati, who started out as a miniscule elf and became a powerful sorcerer.
Well not really in Ganondorf's case, he was born a king to begin with it. Unless you compare how powerful he becomes in the great scheme of things which makes a lowly king of a desert seem like quite a nobody.
In the Hidden Object casual game Surface, a petty criminal named Sid takes over an alternate reality by switching places with his otherworldly duplicate, who rules the place.
In Pokémon Diamond and Pearl and Platinum, Cyrus appears to be this. He is explicitly stated to be a quiet boy who tinkered with machines and lived in Sunnyshore City with his family. Then he grows up, establishes a business empire and a criminal cult, and tries to destroy the universe. And he's twenty-seven.
Another heroic example is of course Samus Aran of the Metroid series. The Space Pirates first encountered her as a harmless girl, orphaned when they attacked her home colony. Years later some bloodwork, warrior training and a suit of Powered Armor has turned that little girl into a One Woman Army with a grudge. She cuts through their soldiers with contemptuous ease, and turns the pirates' technology against them. She can effortlessly hack their data networks and bypass their security systems. She doesn't just wipe out bases, she leaves destroyed planets in her wake. She is the Hunter, the one threat in all the galaxy the Pirates are flat-out terrified of, all because one of their raids over a decade ago left one survivor.
In the Modern Warfare series, Vladimir Makarov started out this way. He was originally just another soldier in Zakhaev's army, but through showing a great deal of skill and loyalty (including saving his life when Price shot him at Pripyat in 1996) he was elevated to one of Zakhaev's top commanders. Then when Zakhaev died, he took over the reins of the more extremist elements of the Russian Ultranationalist party, and from there, the world began to burn....
In Star Wars: The Old Republic, you as a Sith Inquisitor. You start as a slave being sent for some do-or-die Sith training, but by the end of your character quest you'll have killed three powerful Sith lords who got in your way, repeatedly humiliated Darth Thanton by making him kneel before you in front of the Dark Council, and joined the Dark Council. To drive the point home, you can mock and kill the Smug Snake of an overseer who relentlessly bullied you at the start of the game. Oh and you get your own Death star, granted its one of many superweapons but that is still an impressive feat.
Petey Piranha kinda has this. He's the Warm Up Boss in Super Mario Sunshine, and then goes on to appear in the Mario Kart series. He later reappears in Mario & Luigi: Partners in Time as a major boss about half way through the game. He puts up a bit of a challenge but he's not amazingly tough. He also reappears in New Super Mario Bros. 1 as the Boss of World 5. Petey actually poses much more of a threat this time, although if you know what you're doing he's not that tough. Chornologically he actually goes from a semi-decent boss, to a Warm Up Boss in Sunshine, to a full-on boss in NSMB.
In Mario & Luigi: Dream Team, The main antagonist, Antasma, was originally just a bat until a nightmare twisted him and turned him into the evil Bat King Antasma. He then gets trapped in the Dream World (almost literally becoming a nightmare) by the Pi'illo folk and is somehow forced to assume the form of a small bat. He teams up with Bowser and escapes the dream world, going on to becoming one of the harder bosses in the game. He's then betrayed and usurped by Bowser as the main antagonist, and Bowser then serves as the game's true Final Boss. Just ouch.
Garland of Final Fantasy was once the greatest swordsman of the Kingdom of Cornelia, he then decided he wanted to take over his kingdom by holding the king's daughter for ransom, only to be beaten down by the Light Warriors of Lukhan's Prophecy. Flash forward to the end of the game and Garland himself has become the source of all evil, The god of Discord; Chaos!
A late-game sidequest of Borderlands 2 reveals that Handsome Jack was formerly a low-level code monkey by the name of John (or at least called that by the former CEO of Hyperion). Through using his daughter Angel as a supercomputer, he masterminded the events of the first game and took over the reigns of Hyperion after strangling his boss.
Plenty of villains in the Sly Cooper series are this, but one notably subject is the Indian spice lord Rajan from Sly 2: Band Of Thieves. He started out as a street urchin who made it big with spice dealing, but is trying to convince everybody, including himself, that he's royalty.
Starcraft: Kerrigan was originally a soldier turned rebel... unusually strong psychic powers for a human, but nothing too unbelievable. What does she become? The Queen of Blades, the Heart of the Swarm, or, in her own words: "Queen Bitch of the Universe"; she has the entire Zerg Swarm under her control and more sheer psychic power than any other known being in the universe.
Daisy Fitzroy of Bioshock Infinite was just a lowly, but highly intelligent scullery maid. Then she witnessed, and was framed for the murder of Lady Comstock. Descending into the depths of Columbia's slums, she founded the Vox Populi, and through several degrading versions of reality, went from a well meaning revolutionary to a terrorist no better than Comstock.
Comstock himself turns out to be one of these: he's actually parallel-universe version of Booker DeWitt, the game's protagonist, this version starting out a traumatized corporal in the aftermath of Wounded Knee; after having himself baptised into a fundamentalist Christian sect in an attempt to justify what he'd done during the battle, he started preaching, acquiring followers outside the sect - enough to influence the United States government to fund the construction of Columbia. Eventually, through the firepower of Columbia and the Lutece's machinery, he levelled up into an apocalyptic prophet that endangered not only "The Sodom Below," but the rest of the Multiverse as well.
Late in Return To Zork, it's revealed that Morphius started out as a lump of Illumynite rock that was accidentally impregnated by all the evil magic scattered during the Great Diffusion. Having been dug up by the dwarves, made a museum exhibit and titled "The Cluster," it eventually took control of the mage Canuck, and used him to escape underground and build a new empire.
Republic: The Revolution: The player character starts out as the son of middle-class couple. After Karasov has them arrested and likely killed, the character will eventually grow up to be the leader of the faction that overthrows Karasov, and woe betide anyone who gets in his way.
One of the earlier ones: Doom's protagonist starts out as some random marine contracted to protect a research facility in Phobos. One portal screwup and opening of hell later, he singlehandedly saves the base, the human race, and completely wrecks Hell itself.
In the beginning of Dawn Of The Dragons, the protagonist starts out as a simple farmhand picking turnips when a small army of the dragons' beastmen attack his/her hometown. By the end of the day, he/she has killed scores of beastmen, bonded with a baby dragon, and saved the town by pushing an ogre off a roof. The dragon-rider becomes a hero to the people and an object of fear and hatred to the dragons.
In Dark Souls, the Furtive Pygmy was a nobody compared to other Lords. While the other Lords were mighty and awesome godlike beings, the Pygmy was just that: a pygmy. He is even described by the opening narration as being "so easily forgotten". Ultimately, the Pygmy turned out to be more cunning and patient than the other Lords, having come up with a scheme that would ensure that the Pygmy's descendants would one day inherit the world. It's also possible that he became Manus, the terrifyingly powerful lord of the Abyss.