Complex sentence: He also seems to have the ability to travel to and from Neverland via the Jolly Roger, which is how he manages to kidnap Jack and Maggie, setting the primary conflict of the film into motion.
Split into simpler sentences: He also seems to have the ability to travel to and from Neverland via the Jolly Roger. This is how he manages to kidnap Jack and Maggie and bring them to Neverland, setting the primary conflict of the film into motion.