Ken from Digimon Adventure 02 started out as a lonely child who was always in the shadow of his older brother, however after his death a series of events lead to him becoming the evil Digimon Emperor.
Oikawa started out the same way, having Iori's father as his only friend. But after Iori's dad was killed in line of duty, Oikawa promised himself he'd make their dream visiting the Digital World one day real no matter what, and with the help of Myotismon, he becomes a ruthless Magnificent Bastard who almost brought both worlds to ruins in chasing his mad dream.
Kuroda was once an Unskilled, but Strong samurai with a streak for killing. He then makes a deal with the Ayakashi and becomes the series' most memorable villain Kaguro.
Zeta Gundam brings us Paptimus Scirocco, a minor official from Jupiter recruited by the Titans. Over the course of the series he slowly gathers followers and influence, culminating in him supplanting Jamitov and Bosque and seizing control of the Titans. And did we mention he slowly reveals himself to be an amazingly skilled pilot, genius mobile suit designer and extremely powerful Newtype?
In Mobile Suit Gundam Unicorn, Buch Concern, the salvage firm Banagher Links works a part-time job at, is run by the business-oriented Ronah family. The only real notable thing about them at that point in the UC timeline is that they had taken (and bought) their last name from an impoverished line of European nobles. In less than 30 years, that same family would have enough manpower, resources and influence to forge their own realm almost overnight: Cosmo Babylonia from Gundam F91.
InuYasha's Naraku. A bandit fails in his attempt to take over his band and ends up a crippled, burnt wreck of a man destined to live out the rest of his life in constant agony. But his Perverse Sexual Lust for Kikyo grows so strong he makes a contract with demons and is transformed into the Big Bad.
Death Note: Disaffected high school student Light Yagami and incompetent, unpopular corporate drone Kyosuke Higuchi each come across a simple notebook leading each to become notorious mass murderers and, in the case of one of them, GOD OF THE NEW WORLD.
Fullmetal Alchemist: Father, the Big Bad and leader of the Homunculi, began life as a small Xerxian alchemy experiment who could think and act like a human. Eventually, he tricked a slave(Van Hohenheim) into helping him absorb the souls of half the people of Xerxes, gaining humanoid form. Soon, he introduced Alchemy to the rest of the world and became the founder of the entire country of Armestris, kickstarting the manga's plot.
In One Piece, both hero of the show Monkey D. Luffy and his Evil Counterpart Marshall D. Teach/Blackbeard have amassed great infamy in just under a year, from being some no-named rookie on the East Blue, the weakest sea in the world, to having a 400 Million beli bounty, and pegged as a future threat with no end in sight for Luffy, and from being a random Giant Mook for Whitebeard's 2nd Division to killing a high-ranking commander and becoming one of the Shichibukai, the World Government's group of Psycho for Hire pirates, by beating the man formerly in charge of him, and Luffy's Nigh Invulnerable brother for Blackbeard, also still growing too. The rest of the Eleven Supernovas, a group Luffy is sort-of part of with The Lancer Zoro, also counts as well. Granted, this depends on your definition of 'nobody', as Luffy is 1) the grandson of a military hero, 2) the son of a dangerous rebel leader, and 3) the adoptive brother of the former Pirate King's son.
Blackbeard, who busted out the worst among the worst prisoners alive of Impel Down and stole Whitebeard's Quake Quake Fruit power, and declared war on the entire world and everyone in it.
And at the end of the 2-year Time Skip, we find out he's no longer part of the Shichibukai... because in that time he's become Whitebeard's replacement among the Yonkou, the mightiest pirates in the world, each of them powerful enough to make the Marines and the World Government crap their pants.
Buggy the Clown is an interesting example. On his first appearance, he's the arc's Big Bad. Shortly afterwards, he comes back to take revenge on Luffy, and the only thing that keeps him from succeeding is being struck by lightning. He doesn't appear again until a few hundred chapters later, when the Sorting Algorithm of Evil has left him in the dust. But one thing leads to another, resulting in him amassing a powerful crew from Impel Downand becoming a Shichibukai after the time-skip. Yeah, he's a nightmare in the eyes of the general public, but the Straw Hats and everyone beyond the fourth wall knows that he's just a Fake Ultimate Villain…that is, unless he's Taken a Level in Badass during the time skip, but that's yet to be seen.
Another example is Eustass Kid, who managed to get his 470,000,000 Beli bounty by sheer quantity of criminal activities, rather than being regarded as a significant threat to the World Government.
And then it turns out that since the Noah's souls are those of the original survivors of the biblical Flood (notice the name?), everyone on the planet shares their lineage, meaning that absolutely anyone could potentially turn out to be their host. Can you smell the Paranoia Fuel?
Jellal Fernandez in Fairy Tail started out as a slave working under the oppression of a Religion of Evil. Watching his best friend and love interest be brutally tortured and being even more brutally tortured himself, along with subtle brainwashing by a false god, turned him into an incredibly powerful mage whose powers come directly from celestial objects (such as meteors, among other things). He also managed to pull off a perfect Evil Plan, and it was only by devouring Etherion that Natsu was able to summon the power to defeat him.
He is later healed by Wendy and becomes a good guy, although he is still one of the most powerful characters in the series.
Tongpu aka Mad Pierrot from Cowboy Bebop was originally an average man who had volunteered for an experiment to become the ultimate super human, the resulting experiments drove him completely insane and he became a bulletproof, psychotic Serial Killer with the mind of a child.
The D-Reaper from Digimon Tamers. It began as an extremely simple computer program, designed to delete any other program that grew beyond its purpose. Then the Digital World came into being, and the Reaper decided that not only did the Digimon qualify, so did we. It also had an increase in power over its lifespan, going from ridiculously simple computer program to nigh-unstoppable, city-devouring Eldritch Abomination.
Kabuto Yakushi starts out as an experienced Genin who's actually a high-level spy for Orochimaru, but he eventually surpasses his already legendary leader in power and ends up co-leading an evil army of resurrected legendary ninja and Venus Flytrap monsters created from the DNA of one of the most powerful ninja ever.
Big Bad Tobi, who turns out to be none other than Obito Uchiha. That's right folks, the same kid that spent his childhood failing at everything, pining for Rin, feeling jealous of Kakashi, and pretty much being the Naruto of his day, is now the guy who indirectly killed Naruto's parents (one of which was his own sensei) by taking control of Kurama and unleashing him on Konoha, took part in the Uchiha massacre, corrupted Nagato and later Sasuke, co-led the aforementioned evil army against the five great powers of the Naruto universe and is now working to unleash the universe's resident Satan (albeit depowered somewhat), to say nothing of a whole laundry list of additional heinous acts he committed between his "death" and the current story.
Pain was once a normal kid, not even a shinobi as well as a Street Urchin orphan, who with Jiraiya's teachings, became the leader of the most powerful evil organization, killed the original leader of the Hidden Rain, along with his entire network of people who knew him and became a Physical God who destroyed the Leaf village effortlessly.
Gaara's somewhat of a lesser example. As a child, Gaara made many attempts to connect to the people of Sunagakure, all of whom feared him because of his connection with Shukaku. Then his uncle, the only person shown to have ever loved and cared for him at all attempted to murder him under the orders of Gaara's father, the Fourth Kazekage. All of that was enough to turn Gaara into a sociopath by the age of six, and a serial killer by the age of twelve. Naruto's intervention was what would finally set him straight and help reverse some of the damage.
Chirin No Suzu has Chirin, who starts out as a cute little lamb, grow up and become a ram who just looks demonic.
The seemingly cute and harmless Misaki actually became an Eldritch Abomination threat to the multiverse in Tenchi Muyo!. The author had foreshadowed this but everyone had assumed he was joking until it actually happened.
Hunter × Hunter has the Chimera Ants, initially a species of small insects that take on traits of the animals they eat; other than that, they're garden variety bugs. There even first mentioned by a character as a dining delicacy. That's until a rare six foot tall specimen starts eating literally eating everything from animals to Nen users, creating an army of animal hybrids capable of fighting and overpowering the elite officials of the Hunter Organization. And her heir offspring eventually gets so strong, that he's the closest thing to a Physical God before a virus kill him off in order to prevent him from destroying humanity.
The very first villain to appear in The Big O, and one of the few to make a repeat appearance without being an outright Big Bad, is Beck - a no-name low-level crook who wound up working as a go-between and muscle for a secret conspiracy between a Mad Scientist and a Corrupt Corporate Executive. That is, until he betrayed them both and stole the Humongous Mecha they'd been developing in secret, and then proceeded to stomp through downtown in order to rob the Mint like an avaricious Godzilla. Between all the Humongous Mecha and Kaiju that the titular robot has fought throughout the series, Beck's record remains the best, returning to challenge Roger four times - arguably five if you count using his abilities to make the Big Bad and The Dragon's Bigs operational in time for the Grand Finale. And on top of that, he's responsible for releasing the most destructive weapon in the series when he tells Dorothy how to activate Big O's Final Stage. He's very hard to take seriously at ANY point, but really, you probably SHOULD...
And in the manga, he manages to get his hands on a "Gigadeus", completely trashing the Big O and nearly winning in one of the trippiest sequences in the series.
A perhaps more conventional example is Schwarzvald - once upon a time, he was just an Intrepid Reporter, driven to discover the truth about the City of Amnesia while working on his great manuscript in a tiny, run-down apartment. Then his search for the truth drove him to explore the vast network of underground tunnels beneath the city, and what he found made him Go Mad from the Revelation. Next thing you know, he's reappeared covered in bandages, trying to teach people the 'meaning of fear', and generally acting like a combination of The Joker, Scarecrow, and a mummy. With a Humongous Mecha. Which can fly.
Griffith of Berserk began as nothing more than a simple commoner who had big dreams of becoming king. Over the years, he put together a band of thieves, which later became a mercenary army, and then became the highest-ranking general in Midland's army. He then suffered a tragic fall from grace that left him disfigured and physically incapable of realizing his dream...until the Eclipse passed, where he became one of the five demon kings of the Godhand and one of the singlemost powerful individuals in the world.
In Project ARMS, Alice was a sweet girl (albeit a genius, but no one outside of the Egrigori knew of her existence) who took care of the other experimental children and considered Keith White to be her dear "father". She gets shot while trying to see what the outside world is like, and ends up merging with an artificial alien life form, causing her to split into White Alice and Dark Alice. As Dark Alice, she first tries to get the Jabberwock to destroy all of New York, ultimately aiming to get the city blown up by a nuclear bomb. When that doesn't work, she possesses Katsumi, takes over her body, and tries again to destroy the world with her power. She only stops when Katsumi and Ryo offer her love, which was all she ever actually wanted.
In Axis Powers Hetalia, Russia went from being a tiny, weak country under the control of the Mongols and constantly picked on by bigger nations, to being much larger and stronger. This would not be so bad, except that years of revolution and bloodshed mean have left him a Psychopathic Manchild who terrifies pretty much all of the other nations he runs into. Exactly how bad he actually is is uncertain. He's shown snapping and firing on a crowd of protestors in the Bloody Sunday comic and it's implied that he whipped Lithuania when the Baltics were under his control, but he certain is not the rapetruck he's portrayed as in a lot of fanon.
From England's perspective, America could be seen as this. He went from a young child of a colony to declaring independence as a strong country to being a global superpower.
Shion, and, well, every character from Higurashi no Naku Koro ni becomes this at one point or another. Special points go to Shion becasue she is introduced as a minor side-character rather than a main one. What makes this one so horrifying is that the first portrayal of her is RADICALLY different from the portrayal of her as pure evil in Meagashi-hen.
Dio Brando of JoJo's Bizarre Adventure began life as an intelligent, but frustrated (and nigh psychotically ambitious) son of a petty thief in England, 1800s. From there, he quickly became a vampire, a Hero Killer, attempted to raise a zombie army to take over the world, gained the psychic power to freeze time, and even after his death, continues to weigh heavily on the setting. It gets to the point that Dio mentored a From Nobody to Nightmare villain of his own, Father Enrico Pucci, who through him, succeeded in rewriting the entire universe!
Bleach: Done in the Gotei 13Invasion Arc. Ouka Yushima began as a very weak and pathetic shinigami who didn't have the strength to fight in battle or master his zanpakutou. He therefore decided to split himself and his zanpakutou apart into two mod-soul beings that could master his powers. The one mod-soul was the apparent villain Kageroza Inaba and the second mod-soul was the apparent heroine Nozomi Kujou. Kageroza could manipulate space-time, bring the dead back to life and was so powerful he could defeat Ichigo and Yamamoto at the same time. Nozomi could absorb reiatsu, steal the powers of others, combine them with her own power and use it as super-powerful attack, and heal better than even Orihime, she was so powerful she could fight Kageroza even when Yamamoto himself could not. Where the mod-soul powers came from is never explained as none of them were abilities of the original zanpakutou, but when the two were recombined back into Yushima, he was able to combine all these powers to destroy the very existence of Soul Society itself. Being an Ineffectual Loner, he was defeated by both The Power of Friendship and The Power of Love.
In Fist of the North Star, the three Rasho, warlords of the Land of Asura, qualify, since only an Asura who has proven himself by killing hundreds of other warriors is worthy of having a name, let alone rising to the level of Rasho.
Midora from Toriko was a nameless baby born for the sole purpose of being fed to livestock. Now he's one of the most powerful beings on the planet who can literally eat everything around him.
Pretty much any Puella Magi in any version of Puella Magi Madoka Magica could qualify; most of them were ordinary girls upon making their contract, and many of those were so desperate they needed the wish. Upon making the contract, they become powerful magical warriors who tend to treat the rest of humanity as livestock. When they become Witches, they almost universally qualify; particularly the apocalyptically powerful Kreimhild Gretchen, born from someone who described herself as not having any real talents. Homura is a particular example; as we learn, before the series, she was a meek and flustered Ill Girl who seemed fairly weak even after contracting. By the end of The Movie, she's a God of Evil.
Seto Kaiba from the original Yu-Gi-Oh! was, along with his brother, a penniless orphan until he won a bet with billionaire Gozaburo Kaiba and was adopted by him. He then proceeded to take over KaibaCorp in a hostile takeover, remake it as a totally different company, and before his eighteenth birthday, become, along with Pegasus, one of the two biggest names in Duel Monsters. Of course the "nightmare" part comes in with how ruthless and cruel he could be early on, being almost as bad a corporate tycoon as his father (and in the manga version, trying to murder Yugi and his friends in the "Death-T" complex). He toned down a little later, but was still a man to be feared.
Jack Atlas was just "Satellite Scum" before Team Satisfaction folded, and Jeagar offered him a chance to escape. One act of theft and betrayal later, he was on his way to being the King of the Riding Duels, and one of the most intimidating opponents on the circuit. He mellowed a little after losing to Yusei (and a lot later on) but the past remains.
Kiryu was a far darker nightmare. Also a nobody from Satellite, he was the reason Team Satisfaction folded, when he turned to violent attacks on security, leading to his arrest, death after mistreatment in prison, and rebirth as a Dark Signer.
Every one of the android villains from the Bad Future of season two - Aporia, Paradox, Bruno, and Z-One himself - were nothing but four common soldiers in the ragtag army of civilians who were brave enough to try fight the horde of Meklords; they were simply the only ones lucky enough to survive. Unfortunately, their attempt to Set Right What Once Went Wrong turned them into Well Intentioned Extremists who caused Zero Reverse and almost made it worse.
General Esdeath from Akame ga Kill, who started out as a normal, if slightly maladjusted, little girl living in an Arctic tribe with her single father. Fifteen years, the death of her father, and a few mass slaughters later, she's the most feared woman in the entire Empire, a One-Man Army that can create glaciers out of thin air, freeze space and time, defeat entire armies of men twenty thousand strong, and knows a lot more about torture than any normal person should. Oh, and did we mention that somewhere along the way she got a demon in her head that (figuratively) tells her to burn things? When Najenda said she was the scariest person in the Empire, she wasn't lying.