Years ago, when they were young, Jonathan worked as a Pokémon pediatrician in Fuchsia City with his wife Edna as his assistant. He had been thinking about becoming an actual doctor for Pokémon, instead of simply tending their Eggs. However, that would require leaving town for some time to live and study in the city. Jonathan tried to persuade Edna to come with him, but she was reluctant. When Edna finally refused outright on leaving her hometown cause it meant too much to her, Jonathan left her with a note, claiming he loved her dearly, but he needed to seek this avenue.
He boarded the train, never knowing Edna was chasing after him to tell him she was pregnant, and didn't return from that day on. A year after Jonathan left, Edna was given a letter claiming he died in an accident. However, in a state of denial, she didn't believe this and went to wait for him at the station for years.
In the present, May's Squirtle found Edna's locket that she lost when she wanted to tell Jonathan of her pregnancy, and May opened it, sending her and her Squirtle back in time with Meowth. By adhering to Edna's fondest, idealistic wish and May using Squirtle's Ice Beam to turn the rain into snow, effectively delaying the outbound train, Edna now caught up with Jonathan to tell him of their soon-to-be daughter. With the truth revealed, Jonathan remained in town with Edna.
May, Squirtle, and Meowth then returned to the present, now having been altered because of May's actions. They discovered Jonathan was still alive and well, and still worked as a pediatrician. He oversaw the hatching of May's Eevee, with Edna and his granddaughter Katrina aiding him.