Some tips for fixing a Mary Sue, a protagonist that is insufficiently challenged by his or her story.
1. Give the character flaws, ideally one he’s accountable for. Most unchallenged characters have a bevy of strengths but few well-developed flaws. One approach is to play up the character’s strengths so much they sometimes become liabilities. For example, in Point of Impact, Nick Memphis is unfailingly loyal, even though it ruins his career. Virtually any strength taken to an extreme could create obstacles for the character. For example…
- Being too smart could create social obstacles for the character (see Flowers for Algernon or House), impatience with less intelligent people, overconfidence, a willingness to jump to erroneous conclusions on too little information, etc.
- Being too nice could lead to gullibility/naivete, a reluctance to confront someone even when a confrontation is necessary, or a handicap against tougher (and maybe more brutal) foes.
- Being too honorable could result in situations where the character loses because he/she refuses to take the most effective course of action available. At its most cliche, perhaps a superhero stops chasing a gang of villains so that he can defuse a bomb or free a hostage from a deathtrap. But that only affects a scene. More significantly, a villain can manipulate a hero’s sense of honor so that he/she does something that shapes the plot. For example, Cassius draws Brutus into the assassination plot in Julius Caesar by exploiting Brutus’ honor.
- Being too brave could result in reckless mistakes. The character’s overconfidence might get him hurt, and possibly bystanders as well. For example, if a superhero tries to rush a hostage-taker without any sort of plan, hostages will probably get shot.
- Being too committed to one’s goals (even honorable goals) could result in obsession and/or a willingness to sacrifice friends, morals, bystanders, and anything else to achieve the goals.
2. Have the character make some decisions the audience won’t approve of. If the character is so purely heroic that readers will probably approve of every decision he makes, he probably doesn’t have much moral complexity. Usually, that’s not as believable or interesting as giving the characters some human edges.
3. Have the character make difficult decisions. Difficult decisions distinguish the character. If the character is just making banal decisions that 90%+ of the genre’s protagonists would make in the same situation, the plot probably isn’t giving the hero enough room to distinguish himself. Let your hero show how different he/she is with some decisions that most other heroes wouldn’t make. For example, the protagonist in Point of Impact, Bob Swagger, is on the run after he’s been framed for an assassination attempt on the President. The people framing him planted incriminating evidence in his house, but they had to kill his dog to sneak inside. Almost every action protagonist in this situation would probably have started by trying to take down the conspiracy. Swagger starts by breaking into the FBI-occupied morgue where the dog’s body is being held as evidence so that he can properly bury it. It really helps develop his character: the dog is the closest thing he had to a friend and he feels honor-bound to return its loyalty. It also gives the villains reason to panic and ratchets up the tension. If this guy is suicidal enough that he’d risk a high-speed chase with the FBI over his dog, his dead dog at that, what’s he gonna do to them?
4. Challenge the character! Raise obstacles high enough that it will be interesting for the character to overcome them. For example, if your character is the most powerful superbeing in your story, the potential for interesting straight-up action is probably pretty low because he’s more powerful than his opponents. For example, The Watchmen couldn’t have done much with a straight-up duel between invulnerable hero Dr. Manhattan and semi-powered villain Ozymandias. Instead, Ozymandias challenged the heroes with his stealth and subterfuge, buying time so that he could make his survival so valuable to the heroes that they wouldn’t dare to kill him. Another approach would be to try challenging the character in a sphere where his superpowers aren’t very useful. For example, in a superhero romance, a guy that’s used to solving his problems with violence would have to try a very different tack to wooing the girl of his dreams.
5. Have the character face some morally gray obstacles. I would really recommend against making everyone that opposes the hero a straight-up bad person. For example, maybe the character’s friends aren’t 100% supportive of everything he does, maybe his coworkers/bosses have reasonable disputes with the character, or maybe there’s an antagonist whose intentions are pretty pure, etc. If there’s no approach for a character to disagree with the hero without coming off as a bad person, the hero is probably not morally complex enough to feel fully believable. (Hey, even Gandhi and MLK took some flack over their pragmatism).