The conflict in The Golden Compass is simple, it is a battle between good and evil, with the fate of the universe at stake.
"This type of conflict between free-thinking freedom fighters and authoritarian control is common in fantasy and science fantasy stories."
Lyra Belacqua, the young hero, unexpectedly finds herself in a quest for the truth, on the side of good, about a mysterious "dust" that connects all people and parallel universes.
"Lyra sees the Master trying to poison Lord Asriel, warns him, and is then taken into his confidence. However, his comments pique her curiosity about many things such as the church and her own history, which she has heretofore taken for granted. When other children start to disappear into the clutches of the mysterious Oblation Board, she becomes even more curious."
On the side of evil, is the Magisterium, which opposes the mentioning of the dust, they will do anything to keep it from even being mentioned.