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In the prime Star Trek timeline, the USS Voyager returned to the Alpha Quadrant because

a future version of Janeway had come back and equipped the vessel with advanced technology such as ablative generators and transphasic torpedoes.

Both proved to be a massive advantage over the Borg, but chronologically-speaking, the film "Star Trek: Nemesis" is the last we see of Federation technology and/or vessels. I haven't played Star Trek Online or read any of the post-Voyager novels, but I would expect Starfleet to utilize such an advantage - especially with such powerful enemies as The Borg and The Dominion around. Concerns about the temporal Prime Directive wouldn't seem to apply, given that the timeline in question had already been changed and/or erased.

In the Prime timeline, are there any mentions of Starfleet deploying the technologies used by Voyager after its return?

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  • The admiralty ... were making a grave error by not distributing the new weapon design, which had been reverse-engineered from prototypes acquired from an alternate future by the late Kathryn Janeway of the Starship Voyager. Transphasic warheads were quickly proving to be the best defense against the renewed Borg onslaught. The admiralty, however, remained concerned that the Borg would eventually adapt to this seemingly unstoppable weapon, thereby robbing Starfleet of its last effective defense. Consequently, the Enterprise was the only ship in Starfleet that was armed with the warheads. – Valorum Nov 3 '17 at 23:13
  • ST: Destiny - Gods of Night. – Valorum Nov 3 '17 at 23:13
  • @Valorum - might have to read that trilogy, although I'll probably have to start with Titan. Make it an answer and I'll accept. – Omegacron Nov 3 '17 at 23:26
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Not canonically

That episode of Voyager is the last one, and the last television episode set in the 24th century. The only other canon work set in the 24th century that came after it was Nemesis.

They seem to be in a few books

Or so Memory Alpha tells me:

According to the Pocket Books novel Greater than the Sum, transphasic torpedoes were in fact kept by Starfleet as the weapon of last resort to be deployed to starships only when all else had failed against the Borg.

In the novel Lost Souls, set in 2381, during a Borg invasion, the Borg finally adapted to the transphasic torpedoes when Starfleet was forced to send the torpedo specs to the entire fleet following a mass incursion of Borg cubes.

They're in Star Trek Online, but aren't as powerful

They're pretty much a variant on standard torpedo equipment, that results in a 40% shield penetration bonus. Some races have them equipped by default. But it's not a special super dooper weapon like it looks like in Endgame.

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