Jonathan is a male baby seal who expresses himself with simple barks. Sora Naegino discovers him on a beach after tripping over him and secretly brings him to her Kaleido Stage dormitory. His presence is revealed when he encounters performer Layla Hamilton, causing alarm. To fund Jonathan's food, Sora takes a part-time job and enters a juggling contest with Anna Heart and Mia Guillem; Jonathan unexpectedly joins the act, helping them win prize money for his upkeep.

Kalos Eido, owner of Kaleido Stage, eventually permits Jonathan to stay permanently after Sora's persuasion. Jake Benigni constructs a dedicated tank for his habitat. Throughout most of the series, Jonathan is often seen perched on Marion Benigni's head. His performance coordination sometimes surpasses Sora's, creating comedic acts popular with younger audiences.

In the second season, Jonathan partners exclusively with Marion for Kids Stage shows, developing a distinct personality and refusing to perform with anyone else. His bond with Marion deepens, and they collaborate on educational content, teaching seal facts and communication in the OVA "Good da yo! Goood!!," where Sora attempts unsuccessfully to learn seal language from them.

Jonathan appears in additional OVAs and contributes to the franchise's music through the duet "M&J" with Marion on the Kaleido Star Character Song CD. He temporarily perceives Fool, the normally invisible spirit of Kaleido Stage, once under unspecified circumstances.