We introduce the notion of doubly rooted plane trees and give a decomposition of these trees, called the butterfly decomposition, which turns out to have many applications. From the butterfly decomposition we obtain a one-to-one correspondence between doubly rooted plane trees and free Dyck paths, which implies a simple derivation of a relation between the Catalan numbers and the central binomial coefficients. We also establish a one-to-one correspondence between leaf-colored doubly rooted plane trees and free Schröder paths. The classical Chung–Feller theorem as well as some generalizations and variations follow quickly from the butterfly decomposition. We next obtain two involutions on free Dyck paths and free Schröder paths, leading to parity results and combinatorial identities. We also use the butterfly decomposition to give a combinatorial treatment of Klazar's generating function for the number of chains in plane trees. Finally we study the total size of chains in plane trees with n edges and show that the average size of such chains tends asymptotically to (n+9)/6.