Sticky question, its kinda hard to judge without actually reading said plot and world. But some general suggestions would be:
Mentor/Guide Character - If your MC is supposed to be new to everything and thus can't believably solve the mystery alone, maybe introduce a Supporting character to supplement his lack. Not to solve it for him, but to provide some of the pieces of the puzzle that only experience would bring. In one of mine I have a similarly clueless character starting out, but he gets found by a old hand mentor sort that introduces him to things, then gets said mentor taken and has to rescue him, sorta tossing him in the deep end so to speak. Granted thats not a mystery situation, and is basically an Obi-Won trope, but it can bridge that gap.
MC as the "Noble Fool" - Not sure if this is an actual literary term, but its a type of character trait I have always enjoyed. The basic Idea is that your character doesn't know much of anything about what he's caught up in, but by that virtue he has an open and/or unique perspective on the situation that lets him make simple connections that are otherwise obscured to the people more immersed in the world. Tavi in CA pulls this a number of times, being the only one around without Furycraft. The TV show Eureka is built around this idea completely, having the Average guy sheriff in a town full of Geniuses, he's he is able to think outside the box and figure out how to apply various unrelated inventions to solve the weekly catastrophe, when all the scientist get so focused on the science and the intended application, they don't see the other possibilities, but they have to step back and describe it to him in layman's terms, which he then is able to devise new uses and such. or he just remains a bit more grounded than teh rest, like when everyone assumed the kid had gotten caught in the temporal wormhole bubble of doom and launched a giant search for where he may have come out, and everyman sheriff was the only one that thought to check if the kid was hiding in the closet.
Leave him in the Deep End - Sometimes you can get away with leaving the character completely out of his depth, just getting kinda swept along by the events, and still make it work out ok. Niel Gaiman is great with this. The MC's often dont have any clue whats going on until the climax or later. It heavily depends on the supporting cast and the situation to make it work, but the kid just discovering his new powers is a trope that often works with this.
Thats kinda a ramble, hope it was somehow helpful