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At the end of VOY:Year of Hell Part 2, you see Annorax with his wife and he is working on Temporal Incursion Calculations. Does this imply that a significant portion of the Delta Quadrant would be stuck in a sort of temporal loop?

To explain this, Annorax designs and builds his ship and things go to hell because he can never restore the Krenim Imperium as well as Kyana Prime. Eventually, someone stops him and as Voyager did finds a way to reverse what he did and then the loop starts again because Annorax is back on Kyana Prime, working on his temporal incursion calculations.

Following this, it means that Voyager saved themselves this time but doomed everyone in the Delta Quadrant because the only way to stop the threat of Annorax is to kill him or destroy the ship without generating a temporal incursion that resets everything back to 0. Think the TNG episode Cause and Effect. Not the same I know as the Temporal Causality Loop from that episode was due to an anomaly in space.

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I feel that the ending suggests that the new timeline emerged differently.

During the episode Annorax laments not spending enough time with his wife when he could because he was always buried in his work. The final scene shows him at work, but when his wife asks him to join her, he puts it aside to have breakfast for her.

It hints that in the new timeline, he somehow appreciates his what he has more, with the side effect that he never finishes his temporal work, and perhaps things work out happily for him in the end.

The Memory Alpha entry for Annorax also theorizes this:

In this restored timeline, Annorax was again working on a weapons ship, but the evidence suggests that he never finished it, deciding to spend time with his wife instead of work on his calculations.

And:

Since Annorax built the weapons ship 200 years ago, the scene of him planning a temporal incursion at end of the episode should have also taken place 200 years ago. The temporal consequences of this are not clear. Also, since the weapons ship erased itself from history, it is likely that in the new timeline, the ship will never be built.

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    Not canon by most opinions, but the fate of the Krenim is a plot point in Star Trek OnIine. – T.J.L. Apr 23 '16 at 17:11
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The destruction of Annorax's ship didn't revert everything to the way it was before. Voyager's encounter at the Krenim border was different. Instead of being fired upon immediately by a bellicose Krenim vessel, Voyager was hailed by a Krenim official who was curt but polite. His attitude adjustment caused Janeway to accept his suggestion and avoid Krenim space. Since Voyager was an "anomalous component" blamed for at least some of Annorax's miscalculations, even if the superweapon is developed again, Annorax might have better luck achieving his goals. He will at least have different luck thanks to Voyager's absence, which leaves the future of the Delta quadrant unknown and not preordained.

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There should be no temporal loop. The weapon ship erased itself from history at the end of Year of Hell, Part II. This means that an alternate timeline was constructed in which the ship never existed and also never will be (otherwise it would not be erased...).

This is supported by the fact that the encounter between Voyager and the Krenim is different in this new timeline. In this new timeline even if the weapon ship would have been built, the voyager would not be there to destroy it. So also no loop from this side.

Of course this answer is largely speculation, but I tried to stay as close as possible to the facts presented.

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