Re: Endgame is justifed if Kathryn had Syphilis.
Then maybe she hallucinated Chakotay's grave too. Or maybe it's some other dude's, like Billy-Bob Chakotay or something. And naturally the Doc and Barclay know something's wrong and that's why they sent Harry after her.
Or maybe she hallucinated the entire episode and Neelix had actually found some deus ex machina on that asteroid he settled down on, which he told Voyager about, and they got home in five minutes that way. And Admiral Janeway's been crazy for the last 20 years.
Whatever the explanation, it still works as a Brannon Braga mindscrew episode.
Curly: Moe, Larry, the cheese! Moe, Larry, the cheese! (Horses Collars, 1935)