Despite first being named by producers as a Sioux, and later a Hopi, Chakotay was given no tribal affiliation at the start of the series, and eventually was assigned ancestry with a fictional tribe in the episode "Tattoo”.

In the Voyager relaunch novels set after the vessel's return to the Alpha Quadrant, Chakotay is promoted to captain of the ship, but the relationship with Seven has ended.

This led to comparisons with Tonto from The Lone Ranger, and that the inclusion of "Hollywood" versions of vision quests and meditation techniques were contrary to the character's in-universe tribal background.

"[5] Taylor's notes from the early production in July 1993 describe the character as "First Officer – a human native American male, a 'Queequeg' person who has renounced Earth and lives as an expatriate on another planet.

[9] In developing Chakotay, the producers sought the assistance of Jamake Highwater,[11] a writer of more than 25 books of both fiction and non-fiction related to Native American myths and traditions.

[9][12] Highwater was a controversial choice of advisor, having been exposed by Hank Adams and Vine Deloria, Jr. as taking a fake Native American ancestry to sell books.

He described the casting process for the part of Chakotay as difficult due to the lower numbers of Native Americans who were in the Screen Actors Guild.

[17] The casting process came down to two actors, and the producers decided on Robert Beltran, who until then was best known for appearing in the soap opera Models Inc. and was of Mexican heritage.

[17][18] Beltran was not familiar with Star Trek before auditioning, and went along on the strength of the "Caretaker" script which showed the character becoming the second in command of Voyager after both their vessels are stranded in the Delta quadrant.

Beltran felt that Chakotay was one of the characters alongside Harry Kim, Tuvok, and Neelix who were left behind by the new writers, who tended to concentrate on Janeway, Seven, and The Doctor.

[28] Beltran explained that it did not affect his relationship with the other actors, and in the end, he felt the producers decided to keep him on the cast as it did not make "very much difference, except to a very, very small percentage of fans who maybe didn't like what I said.

[32] At the age of 15, Chakotay visited Earth with his father, who sought to find his tribe's ancestral home in Central America and the descendants of the Rubber Tree People.

After the Federation starship USS Voyager is also trapped in the Delta Quadrant and Tuvok was revealed to be a Starfleet agent, Chakotay agrees with Captain Kathryn Janeway (Kate Mulgrew) to work together to find two of their missing crew.

Chakotay was given a provisional rank of commander and named executive officer, the second-in-command of the vessel and the crew seeks to return home to the Alpha Quadrant.

The incident occurs while Tuvok and he were investigating a dark matter nebula, and he sought to prevent the ship from returning there, as an alien species wants to feed on the crew's neural energy.

After Voyager enters the nebula, Chakotay possesses Neelix (Ethan Phillips) and guides the ship out using a medicine wheel as a map.

The two began to show signs of affection for each other, but their stay is short-lived after Voyager under the captaincy of Tuvok agrees a deal with the Vidiians for a cure.

Voyager attempted to extract Seska and the child, but it was a trap and resulted in the Kazon boarding the vessel and stranding the Federation/Maquis crew on a nearby planet.

While Tom Paris (Robert Duncan McNeil), The Doctor, and Lon Suder (Brad Dourif), along with allied Talaxian forces, sought to retake Voyager, Chakotay was instrumental in the crew's survival on the planet.

[51] In "Unforgettable", he falls in love with Kellin (Virginia Madsen), a member of a xenophobic race who have developed a technology to prevent others from forming long-term memories of them.

Chakotay's mission was to continue exploration of the Delta Quadrant after Voyager's return, but his ship fell through a time rift into the future where it was captured by the Vau N'Akat who blamed the Federation for the destruction of their home planet in a civil war.

At the end of the first season, following the destruction of the Protostar, a new temporal rift is opened through which Starfleet receives a distress call from Chakotay 52 years into the future.

However, they accidentally change history, allowing Chakotay and Adreek to escape with their ship through the rift, sending it elsewhere and creating a temporal paradox that starts destroying the universe.

With the help of Wesley Crusher, the cadets eventually find Chakotay in the present where he has been marooned for ten years on another planet, becoming a broken man following the loss of his crew and hope.

[62][63] In 2016 Chakotay was ranked as the eleventh most important character out of 100 of Starfleet within the Star Trek science fiction universe by Wired magazine.

[65] In July 2019, Screen Rant ranked "The Fight" as one of the top five worst of the series, singling out Chakotay as a major problem in the show noting how he did not really fit in, and had poor development.

This was highlighted during the episode "Faces", in which one scene showed Janeway, Tuvok, Harry Kim, and Chakotay in a single camera pan.

",[76] it did not take a more prominent role until later in the series, with Star Trek: Deep Space Nine exploring the Bajorans' beliefs and Voyager concentrating on those of Chakotay.

[77] These included vision quests, and other interpretations of Native American culture which were described by critics as showing a "very Hollywood version of Plains-culture religion".

[1] The appearance of a medicine wheel in the episode "Cathexis" was described by Sierra S. Adare as showing Chakotay as a "'good Indian' in the classic Pocahontas sense".