In Star Trek Online, episodes are player mission chains (also known as "quests"). They were called episodes rather than mission chains or quests mainly due to the Star Trek TV series and how they impacted Cryptic's influence on how to design and tell a story in-game. They stated that their content writers approached the content as if they were writing an episode from the TV shows. This seemingly allowed Cryptic to develop better stories for the game in relation to how they play, look and feel.
Episodes in the game are written to advance the overall story; however, some episodes will be standalone and will not have much to do with the main story. This is by design as Cryptic has stated that the TV series often featured side-stories that were not directly part of the main storyline.
 Story episode/mission list
- See main article: List of missions
Episodes always consist of more than one mission. Most of the content in Star Trek Online is episode-based and features extra objectives to complete after finishing the original outlined objectives. Other missions are singular and have one goal or one set of goals that has no follow up objective(s), such as a sector patrol mission.
Most of the main storyline in the game revolves around the Federation's conflict with the Klingon Empire in the year 2409. The story, and subsequently the episodes and missions, are set in the prime timeline and continues events from Star Trek: Nemesis. It also features some story content from the new Star Trek film by J.J. Abrams. However, since most of this story was set in a newly created alternate timeline, the game doesn't include things like the destruction of Vulcan.
Episodes and missions follow a very similar structure to most other MMORPGs. They are received from a non-player character (typically abbreviated to NPC, plural: NPCs, not to be confused with NPC's), added to your assignments, and then carried out by the player. The player then contacts the original NPC that gave the mission (optimally via the "Hail Starfleet" button) to receive their reward(s). Some content objectives are automatically given to the player upon entering a certain area, such as Starbase 24, or engaging an enemy signal content in sector space.
Rewards for completing episodes and missions are typically skill points and expertise. Some missions also award Energy Credits as well as Dilithium. Sometimes they give the player extra rewards, which includes (but is not limited to): a new bridge officer, a piece of armor or a new starship item like a Deflector Array or Cannon.
Most episodes and missions take quite a long time to complete. They can, for instance, take anywhere from 30 minutes up to 2 hours to finish, whereas singular missions — which are generally shorter than episodes — can still take the player up to 45 minutes to complete.
 Repeated Content
There is a lot of content that is repeatable in the game. This means that the player can repeat this mission indefinitely and receive the (sometimes reduced) reward for completing it multiple times. This repeatable content tends to be missions that are not directly related to the storyline.
Some of the non-repeatable content can be repeated by helping another player complete it. This allows you to receive rewards like you originally did when you completed this yourself but they will mostly always give you a reduced rate of rewards. If the episode or mission also offered a special reward (such as an item), however, you will typically not receive it again.
 Replaying Missions
- See also: Episode replay
Most missions can be played again in random order once they are completed. In order to replay a mission, simply open your Mission Journal and select the episode, i.e. chain of missions, and then the mission you want to experience again. Most missions offer new rewards when played again.
 Additional Content
Cryptic has stated that they will continue to add to the storyline in the game with more episodes and missions periodically added to the game via content patches.