Star Trek Online's first incarnation was under development at Perpetual Studios. Perpetual begun the process upon acquiring the Star Trek license in 2004. The game was set in the 24th century --the era of Star Trek: The Next Generation--but the developers left the door open for possibilities to visit the time of the original Star Trek, Star Trek: Enterprise, or the locations of Voyager or Deep Space Nine. Star Trek Online under Perpetual was described as a mix of action-based gameplay while still being true to the Star Trek spirit.

Players could create a character in Starfleet and perform a series of quests and other tasks, with the potential to rise to the captain's rank and command his or her own ship. Notable team members who worked on the game included Andrew Probert, who worked on Star Trek: The Next Generation as an illustrator. Images released in 2006 introduced the look of character designs and also hinted at ship interiors being in the game, a subject that was debated and previously unclear.

Development continued, with regular dev blogs from the team. In late 2007, Perpetual canceled its other big MMO, Gods and Heroes, to focus, it said, on Star Trek Online. Perpetual's financial and legal issues led to a liquidation and reacquisition. Later that year, more images were released, along with statements that the game would potentially become a more casual title as well as adopting a microtransaction-based financing model rather than a subscription. Eventually, in early 2008, P2, the reformed company from Perpetual's assets, shut down. Star Trek Online's license and images, minus Perpetual's code, were transferred to the new developer, Cryptic Studios.