According to an interview by GameSpot with Cryptic Studios' executive producer Craig Zinkievich, there will be references to several famous storylines, ships, and characters from various Star Trek shows. To get a high level character, you can buy STO Power Leveling service.

One confirmed Star Trek film reference was revealed when Zachary Quinto announced, at the 2009 Spike TV Video Game Awards, that he will be "the voice of Atari's new 'STAR TREK ONLINE' game".

A system called the "Genesis System" will allow Cryptic Studios to algorithmically create and add new star systems to the game. Players will be able to explore these uncharted star systems, and might find content which opens up new resources and technologies. Players may find races with various special abilities who can be recruited to the players' crew.

The game will feature two very different combat systems. Away-team missions will feature fast paced "run and gun" combat. Space combat will stress the long-term tactical aspect of combat between capital ships, in concert with the Star Trek storyline, and will entail positioning, shifting power between weapons and shields, and finding various weaknesses.