Several years later after the first Star Trek series had ended, the crew appeared again in an animated series. It continues more of the adventures of the original series and is presumably in the fourth year of the five-year mission.

Star Trek now takes advantage of the unlimited special effects provided by animation to provide more landscaping to alien planets, and alien ships, and more elaborate adventures and new technology. The crew uses life support belts whenever needed, whenever they are in space, underwater, or whenever the life support fails to operate. The deflector shields are now visible, and the Enterprise looks closer to when it gets renovated, but still has many of the features that the Enterprise had when we first see it in the 1960s. Other examples of advanced special effects are when the the crew shrinks to 1 cm, and there are giant identical duplicates of people, including Spock. A giant fire-breathing two-headed dragon also appears. They also use the animation effects to introduce different aliens, such as aliens that lived underwater, and aliens that resemble insects and plants. There are more aliens seen in Starfleet. One historian is a humanoid bird.

More crew members are introduced, such as the felinoid M'Ress and the tripedal Arex. However, Checkov and Rand are not seen, although Walter Koenig is a writer for the series.

There were sequels to many of the things that happened earlier, including several stories that were screened but not aired. One of those stories involves more of the furry tribbles, and there is another story involving conman Harry Mudd.

There is an on-going debate by many people that this series, and many story lines that are introduced in novels, are not considered to be "canon" with the remaining Star Trek series, despite the many facts and examples of the Star Trek references and technology and characters. They continue the stories from the first series, and even is adapted from some of the cancelled scripts. Many elements of this series are used in the following Star Trek TV shows and movies. We get to learn that James T. Kirk's middle name is Tiberius, Spock's mother is named Amanda Grayson, Robert April is the first captain of the Enterprise, Uhura is now seen in command of the bridge of the Enterprise, and the saying "Beam us up, Scotty" is also heard spoken on screen for the first time. The first holodeck is also introduced. InStar Trek: The Next Generation, Sarek mentions some of the events that happened in this series, and some of the elements used in this series are also seen in comic books and novels. Peter David writes some of this, and Lt. M'Ress is in one of the Star Trek: New Frontier stories.