Jonathan Crane is the son and only living child of Ethan Winthrop and Gwen Hotchkiss.
Gwen is unaware that she is already several months pregnant when she leaves her husband, Ethan, and moves away from Harmony after finding him in bed with his ex-fianc๏ฟฝe and constant love-interest, Theresa Crane. Though she has experienced symptoms of pregnancy, she is not suspicious; she believes that she is barren after the stillbirth of her daughter, Sarah, three years previously.
Gwen is already in her second trimester when she discovers that she is pregnant. She decides not to tell anyone of her pregnancy, however, fearing that Ethan, among others, will believe that she is using her pregnancy to win him back. Gwen gives birth to a son on May 11, 2000; she returns to Harmony a month later in order to finalize her divorce.
After Ethan is poisioned and falls into a coma, Gwen realizes that she is still in love with him and regrets their divorce. Gwen anxiously waits for Ethan to emerge from his coma, but is called away with news that Jonathan is ill. Once he has recovered, she returns to Harmony with him and introduces Ethan to his son ๏ฟฝ Theresa has just told Ethan that he has a son, but was referring to their child, Little Ethan, instead of Jonathan, as Ethan assumes.
Ethan and Gwen bond over their son, naming him Jonathan after his maternal grandfather. However, numerous characters begin to question Jonathan's health ๏ฟฝ both Ethan and Rebecca comment that Jonathan sleeps too much, and Ethan and an ICU nurse observe that Jonathan looks a bit strange at one point. When Jonathan spikes a fever of 105๏ฟฝ, Ethan and Theresa rush him to the hospital, despite Gwen's denial-induced insistence that he is fine. At the hospital, Vincent Clarkson changes the dosage of medicine that Dr. Russell has prescribed for Jonathan, hoping that Jonathan will die and the medical review board will assume that Eve had prescribed the wrong dosage while under the influence of alcohol.
Jonathan receives a dosage far too high for an infant and barely clings to life; doctors insist that he needs a special treatment, but Gwen refuses to authorize it, insisting that Jonathan will be fine and refusing to let the doctors who nearly killed her son treat him any longer. Ethan finds himself unable to authorize the treatment because Gwen has not listed him as Jonathan's father on the birth certificate, but he is finally able to understand that Gwen's reluctance comes from denial and fear that Jonathan will die as Sarah did. Gwen authorizes the treatment in just enough time to save her baby.
Jonathan is still ill, however; doctors now report that he is in liver failure and is in dire need of a liver transplant; only a close blood relative stands a decent chance of being a match for donation. Neither Ethan nor Gwen, nor his parents or her father (due to Rebecca's excessive drinking, her liver was not considered), are a match, leaving only Theresa and Ethan's nearly three-year-old daughter, Jane, as a possible donor. Due to Jane's young age, however, doctors are reluctant to allow her to serve as a donor, and Theresa begs Gwen to allow her to tell Ethan that her son, eleven-year-old Little Ethan, is also his son and thereby also a possible and more suitable donor. Gwen refuses, however, and when Jane is found to be a match, and doctors are sure that the procedure will not adversely affect her health, Ethan and Theresa agree to let Jane serve as Jonathan's donor.