Jonathan has never wanted anything more than to be one of the gang. Any gang. Sadly, he was an outcast in high school, far beneath the notice of the popular crowd: short and nerdy, he never stood a chance. This search for acceptance led him first to the brink of suicide, thwarted by Buffy, when it failed, and later into the villainous Trio.
Warren and Andrew are the first people who seem to completely accept him as one of their own. Sadly, they also later betray him - or Warren does. Andrew tries to and fails, and he and Jonathan run away to Mexico, relying on each other for lack of anyone else.
Despite his status as former semi-villain, Jonathan is a good man. He dies trying to do what he believes is right, sent the knowledge in dreams, but to the last, he's misled - this time by the First. His work in digging up the Seal only allows Andrew to murder him. He will continue his search for acceptance in Milliways, while working through things with Andrew and perhaps Warren.