In another universe, a young girl stumbles upon a plot in the kidnapping of children by a religious organization called the Magisterium, who will stop at nothing to ensure the continuation of their doctrine and hold over the world they live in.

Given that this is your logline for an existing film, The Golden Compass.
Was the Magisterium a religious organisation? Given that the sequel was stopped because of religious group (catholics) I'd leave out the religious aspect completely.
(Don't you think that Lyra's father, Lord Azriel is a bit of a 007 character?)
I'd suggest following the logline:

The prophesized leader of the rebellion begins the battle against the Magisterium; to announce her father as a hero, with the Witch Queen, the Gytians, an aeronaut and the armoured bear Lorek Byrnison.

By stating who is in the battle, a greater level of interest and the want to know more can be attained.

Sounds like a terrific tale, Justin!

It's a little long, I think, for a tag line, and there are a couple of things that come out straight away.

I don't think we need "In another universe" -- assuming that the book will be marketed as sci-fi or fantasy, that is pretty much a given.

I don't think you need "called the Magisterium" -- we'll find that out when we start reading, right?

So, already it becomes tighter and clearer. Adding a couple of other changes I'd suggest:

A young girl stumbles upon a plot in the kidnapping of children by a religious organization, which will stop at nothing to ensure the continuation of their doctrine and hold over their world.

A couple of other thoughts: "stumble upon" tells us the character passively find out about this plot. I'd consider "a young girl discovers", perhaps -- it's tighter in any case.

I also tightened "the world they live in" to "their world."

Also, "stop at nothing" is a cliched phrase. Can you say the same thing with some different language?

Jeff