If the quad wants, he/she can bail off of the tree and haunt, help, or go into enemies bodies and control them. In the pictures it shows the stages. When the spirit is in the crystal, he/she is also guarded by a Spirit Tree Seed, which is a boney, holey thing.
Every animal can sense whose spirit is in whose crystal by just looking at it. The animals can also speak with the spirit. When a quad dies and he is in a crystal he has the choice, of, when ever he wants, can enter The Spirit World.