Voyager: Why the Maquis were never imprisoned

Star Trek: Voyager was unique in its combination of Starfleet officers and crewmembers and the rebel Maquis who fought against the Cardassians and became the enemies of Starfleet. When the two had to come together, the tension didn’t last for very long, though fans still wondered why, after Voyager had established contact with Starfleet, that Janeway wasn’t told to arrest all of them and put them in the bring. In fact, Roxann Dawson, who portrayed B’Elanna Torres had that idea after  the Maquis were finally defeated.

However, according to executive producer, Jeri Taylor, (in comments she gave in Star Trek: Voyager A Celebration), the producers never saw the conflict between Starfleet personnel and the Maquis people as a major element of the series. Taylor said that kind of conflict would have violated something Gene Roddenberry felt strongly about.

"…in the 24th century people wouldn’t simply fall back into conflict based on what had happened in the past. They needed to pull together against the larger obstacles. We never wanted Chakotay to oppose Janeway for the sake of it.”"

This, of course, differed from Star Trek: Deep Space Nine where the Maquis were actively hunted and imprisoned. In that series, they weren’t working together, and the focus was on the criminality of the Maquis. In Voyager, though, they had to work together as a crew.

While there was no explanation as to why Starfleet didn’t instruct Janeway to place them in the brig for their criminal acts, we can assume it was because Starfleet knew Voyager wouldn’t have gotten back to Earth safely without everyone on board cooperating. On top of that, by the time the connection was made between Starfleet and Voyager, the Maquis had already been defeated. The ship had a united crew that worked together to get home, and that kind of coming together was what made Voyager unique.