There are some different diagnoses that might be appropriate here.
You've clearly established how the character came to be involved, but now that he is, he doesn't seem to actually be very helpful. He's kinda there all the time, and occasionally he just happens to have precisely the right skill for saving the day - but most of the time, he's just kind of hanging around; he doesn't really have anything important going on with him and he isn't really able to actively participate in the plot.
Examples (Debatable): Xander (Buffy the Vampire Slayer), Harry Kim (Voyager), Mary Jane (various Spider-Man incarnations), Lt. Ford (first season of Stargate: Atlantis).
Solutions: I'm not crazy about the "easy fixes" to this one, which include:
- Force the character into the spotlight by creating scenarios which are tailored specifically to the character's unique strengths. These tend to be pretty implausible ("Who would have guessed we'd need a left-handed sanitation inspector in order to defeat the Demon of Frozen Eternity, ha ha!"), and they don't serve their purpose - they demonstrate that the character isn't totally useless, but in every plotline that isn't deliberately created around him, he's still pretty useless.
- The character becomes upset over his own ineffectiveness. This gives him a stake in everything going on - because he now not only wants to succeed; he wants to prove himself to others. This can work, but it can also be kinda whiny and insecure. It's generally not very interesting on its own.
- The character is cast as the comic relief, or simply a commentator. If you accept that the plot isn't meant to revolve around him, then a cool, funny character is fine for just adding fun commentary and reactions along the way. He's an observer, not a player. As long as you write him appropriately and don't create the impression that he's a central character with choices to make, you can keep his voice in the story.
A more drastic approach is to have some incredible change befall that character - something that forces him to evolve into something more tightly tied into the story. The reason I bring ST:A's Ford as an example is because after season 1 (which he spent being generally present, sweet, and utterly uninteresting), he gets overdosed with an alien enzyme; he turns into a super-soldier - who's also addicted to the enzyme as though it's a drug. Note this passage in the Wikipedia description:
Ford was a regular in season one. Since the series producers and the actor himself felt that Ford had not worked as intended and was highly underused, the writers came up with an idea to make the character more important in a recurring role.
If the Stargate example isn't clear, imagine if Mary Jane or Lois Lane stopped complaining about being on the sidelines of their superhero's lives, because they suddenly got superpowers themselves - stepping into the main stories. (Note to actual comic book readers: I'm assuming this has probably actually happened once or twice. (At least I hope so, because the solution I heard about was "One More Day".))
At any rate, if this is roughly the situation you're facing, then this character needs to be stepped up or stepped down. If his character concept doesn't have an intrinsic connection to the plot, then either force one on him, or take him offstage.
Maybe your character has got lots to do - it just isn't really related to the plot. In this case, possibly that character has their own story to tell - and by trying to shoehorn him into a different one, one that isn't about him, you're kind of squishing him.
The warning sign here is if you have scenes to write for him, but they're not scenes that advance the real plot - they're developments and repercussions centered around that character, not around the story.
If this makes sense to you, maybe you need to put this character aside for a moment, and reconsider his role in your story. Maybe you want to write his story first - give him a chance to flex - and come back to this piece later. At any rate, don't let a character overwhelm your story unless it's his story (or you decide you want to make it his story).
An example I can give here is the Fool in Robin Hobb's Farseer Trilogy. Hobb has described how the character of the Fool turned out to have a life of his own, to demand more and more involvement - and that's fine. But she kept the Fool secondary to her main plotline; she made sure the Fool's relation to her protagonist was what she focused on. The Fool has stories of his own - and a later sequel, the Tawny Man Trilogy, made him much more of a protagonist than he was in Farseer.
If you want to keep the character, you can do the same - let your character grow, but direct his growth into the things that are important to the story. How does he react to what's going on? What in the plot is important to him? What are his stakes in the conflict? How does this inform his interactions with the other characters?
And if you conclude that he really isn't interested in the primary plot - then it's time to let him go.
Sometimes, a character seems like he should fit in perfectly - but in practice, he never quite does. He relates to the plot, but he's not interested in affecting it, or he's going in different directions than everybody else. He's playing, but he's not playing with the rest of the team. His interaction with the other characters is nonexistent or uninteresting.
In this case, all you're missing is a good hook to tie him in. Once he's in, you'll know what to do with him - you just need justification to keep him involved and engaged. Here are some questions you can ask in order to find - or create - a hook.
- What's the character's stake in the plot? The moment he has something he cares about, he's got reason to be involved - and to act. He might work at cross-purposes with your protagonist (say, a rival), or he might be interested in some side-effect of the plot (say, he collects monster-bones for magic spells, so he follows around the hero, who's a monster slayer).
- Personal relationships promote interaction. Does the character have a relationship with any of the characters that compels him to action? Could he be a lover, a suitor, a sibling, a mentor, a student? Any of these give him motive to be interested and involved in pretty much anything the main characters do.
- What guarantees his commitment? Characters are easier to control if they're committed to the plot - if they can't go, "ehh, forget this, I'm going back home to watch TV." You've got a carrot in terms of a stake in the plot; what's the stick that keeps him from ever backing out? Could he be running away from something? Obligated to somebody? Dying? Determined to win a preposterous bet? Handcuffed to the protagonist?
I've given you a lot of options and analysis here, but the tools are pretty similar each time - so I hope this is helpful even if your case isn't quite any of these. You're always asking yourself: Why isn't this character currently working? What would make him more involved? How can I connect him more deeply and fundamentally into the main action? And if you can't connect him well, then you sideline him or take him out.
Hope this helps!