Messiah Creep

Given sufficient running time, the protagonist will invariably evolve into either The Messiah or the Messianic Archetype, overriding any previous characterization.

This seems likely to happen to a character who was previously The Ditz or The Fool, or otherwise fell into This Loser Is You category. More cynically, it may occur because characters otherwise lacking any genuine positive qualities can only compensate by the "kindness of their heart". It can also occur as a result of exclusively positive Character Development. A character actually learns their Aesops and overcomes the flaws in their personality, but creators are loathe to have them develop new flaws, so they end up perfect.

This does not mean a Messiah who's a creep. Although that also happens.

Examples of Messiah Creep include:

Anime and Manga

Kenji from 20th Century Boys starts out as The Everyman, but by the end is a full-fledged rock and roll messiah.
Sailor Moon is a clear-cut example: Usagi was initially The Chick, but became and was actually called The Messiah by the third season. Coupled with Minako's Flanderization, it caused them to swap roles, promoting Usagi to The Hero and reducing Minako to The Chick.
Kira Yamato in Gundam Seed essentially became one of these in the sequel series Destiny, earning the moniker "Jesus Yamato" in the process.
Kei Kurono in Gantz does this starting out all the way from Jerkass Designated Hero. Although it's less drawing on the "kindness of their heart", and more tatooing "What would Kato do?" to the inside of his eyelids as part of his Character Development.
Naruto is also becoming a clear cut example in the more recent chapters.
- Somewhat lampshaded as he lately started calling HIMSELF a "savior."
Shibuya Yuuri of Kyou Kara Maou starts out an ordinary idiot who had super powers if he got really, really mad. Over the series he conquers racism, defeats the Sealed Evil in a Can, purifies a corrupted deity, and develops in a competent monarch, albeit one that is only still alive because of his loyal advisors.

Comic Books

Doc Savage is a really good doctor (creating antibiotics for plagues) who becomes a REALLY good doctor (making the blind see, the lame walk, raising the dead from 3000 years ago) after just a decade's experience. Then he falls from grace by fracturing his skull and goes to Hell to fight the devil.
According to Alex Ross, Superman started out in The Golden Age of Comic Books as a strongman akin to Samson. By the Silver Age Curt Swan era, he had come to be much more representative of a heavenly savior. And, of course, he died and came back in the '90s.
- In Kingdom Come, Superman also fulfills the Second Coming aspect.

Fan Works

In Shinji and Warhammer40K, despite his best efforts, Shinji appears to be turning into the God-Emperor of Mankind. Better Than It Sounds by a long shot.
Fairly English Story: Considering who we're talking about, it makes sense, but the exploration of it in Minato's character development is very interesting to study, considering the changes his personality gradually makes over the course of the story.
- In My Life Is a Goddamn Mess, Minato slowly evolves from an Emo Teen with the story's title as a Catch Phrase into The Messiah.

Literature

Harry Potter gradually becomes this, particularly blatant by the end of the seventh book.
- Although, right from the first book Dumbledore was beginning to sign that Harry would have Messiah qualities.

Live Action TV

Heavily invoked in Babylon 5 with G'Kar. After a lifetime as a Narn resistance leader and soldier, filled with hate for the Centauri, he experiences a revelation that causes him to completely rethink his own beliefs and values. After the Shadow War, he becomes something of a teacher and philosopher to the Narn colonists on board; his private writings were even taken and published (entirely against his will) as a new holy book, which sweeps through the masses. More and more, to G'Kar's irritation, the Narns look to him for spiritual answers rather than seeking them out for themselves. He wants to teach them, but is very uncomfortable taking on a Messianic role where his every word is dissected for some deeper meaning. Eventually, he leaves the station to travel the galaxy, both to find those deeper answers for himself and to give his people the chance to do the same without his interference.
Daniel Jackson in Stargate starts as a TV Genius, naturally assumes the role of The Smart Guy when the titular team of Stargate SG-1 is assembled, but by season four, becomes The Messiah while the role of The Smart Guy is almost completely delegated to Samantha Carter. It certainly doesn't help that he later actually ascends. Well, for one season. And then does it again, but only for one episode.
The Doctor began as a selfish, irritable old man on the run from his own species. He has since saved multiple universes multiple times, is viewed as a mythical, god-like being by numerous people throughout time and space (and may actually be one), and causes the most terrifying creatures in existence to crap their proverbial pants in terror at his sheer presence.
- The new series put him in much the same position, having just escaped the Time War.

Video Games

Stocke from Radiant Historia starts out cold and aloof from his subordinates, but becomes more wiling to form lasting emotional connections with other people over the course of the story. He remains somewhat stoic, but is completely dedicated to their well-being, and his desire to protect them eventually extends to the rest of Vainqueur's inhabitants as well. By the end of the game, he actually sacrifices himself in the Ritual in order to protect all the races from the continent's desertification.

Webcomics

Torg from Sluggy Freelance has gotten a bit of this treatment as the series has gone on (particularly during "That Which Redeems"), but his Cloudcuckoolander status always reasserts itself eventually.

Western Animation

Aang in Avatar: The Last Airbender begins as The Fool, evolves into The Messiah. Though to be fair, this had been what he was originally supposed to do before running away and being frozen for a century.
Flash from Justice League, though this is a slightly unusual example, since he's only one of seven equally main characters and therefore not technically the hero. At least, no more so than the other six. He starts out as the immature rookie of the group, with a leaning towards the idealistic approach and a tendency to hit on people. But this is followed by the implication that his influence is keeping the League out of Knight Templar territory and a reoccurring tendency to try and help everyone that eventually leads to marking him as The Messiah.
At the start of Ben 10 Alien Force, the only thing Ben had in common with Sailor Moon was her Transformation Sequence. He's since adopted her ability to heal the villains' victims with the Empathic Weapon and Wide-Eyed Idealist hatred of sacrificing anyone.