Jonathan is an android butler created by Rex Owen's parents, Dr. Ancient and Mrs. Cretacia, to serve their family and specifically to protect their son, Rex. Prior to the events of the series, Jonathan assisted the Ancients aboard their timeship, the Backlander, during a mission to the Mesozoic Era. When Rex was born, Jonathan was tasked with guarding the infant. However, during a confrontation with the villainous Dr. Z, Jonathan and the Ancient family were separated in a time vortex, causing the android to be thrown into the distant past and lose his memory and functionality for a significant period.

During the first season, Jonathan appears in a damaged and malfunctioning state, serving primarily as a background gag. With his head turned upside down, he takes on various odd jobs around the world, appearing as an airplane pilot, a tour guide, a dancer, a chef, and a train conductor. In these appearances, his damaged state results in a personality that is inconsistent and erratic, ranging from clueless and kind to prideful. It is during this time that the villain Seth tracks him down to extract vital data from his memory banks, leaving Jonathan defenseless. After protecting the D-Team from a dinosaur attack, he is brought to the D-Lab, where he is repaired. With his head returned to its correct position, he begins to regain his memories and reveals crucial information about the future and the true nature of the Dinosaur Cards.

By the second season, known as Mesozoic Meltdown, Jonathan has been fully repaired and assumes a more critical role in the story. His core motivation is his unwavering loyalty to his creators and his programming to protect Rex. He serves the D-Team and even their former rivals, the Alpha Gang, by piloting the Backlander through time. His primary function is to navigate different eras, from the Cretaceous Period to various historical settings, as the group pursues the Cosmos Stones and battles the Spectral Space Pirates. Although his personal story involvement diminishes compared to his central role at the end of the first season, his ability to operate the timeship is essential for the entire plot, providing the means for the group's episodic adventures through history.

Jonathan's key relationships are defined by his original programming. He is fiercely loyal to his masters, Rex and the Ancients, and obeys their commands without question, even when those orders conflict with his personal desires, such as following Dr. Ancient's directive over Rex's wishes in a critical moment. He acts as a dedicated guardian and resource for Rex and his friends. His development across the series is significant, transitioning from a broken, comedic, and nearly useless figure into a competent, reliable, and powerful protector. In the first season finale, he demonstrates notable abilities, including superhuman strength and agility sufficient to battle advanced robots and dinosaurs. He also displays extreme durability, capable of withstanding powerful dinosaur attacks like Fire Scorcher and Volcano Burst and remaining operational for a short time afterward. In the second season, these abilities are largely applied to operating and repairing the complex time-traveling ship, solidifying his role as the indispensable mechanic and pilot for the team.