Warning: Wikipedia contains spoilers.
The character of Jonathan has been present since quite early in the show. He was always portrayed as shy, difficult, and socially isolated, with resulting problems. For example, in the Season Three episode Earshot, he came close to committing suicide, while in Season Four's Superstar, he used magic to alter the history of the world and make himself a superhero.
Most of Jonathan's episodes occurred in Season Six, where he was a reluctant member of the Troika crime gang. However, troubled by the increasingly evil behaviour shown by his two confederates, he eventually switched sides and helped save Buffy's life.
Jonathan was killed in Season Seven by Andrew, who was under the influence of the "First Evil".