Star Trek: 10 Moments That Confirm J/C (Janeway & Chakotay)
7. Allegorical Time Keeping
Captain Janeway hadn't realised it at first, but to defeat megalomaniac Annorax and his high-tech manipulations of the timeline, she was going to need the decidedly lower tech of the 19th century replica(ted) silver pocket watch that Chakotay had offered her on her birthday. Her order to "recycle" it was an order Chakotay (once more, but thankfully) disobeyed.
There never was a "Captain Cray of the British Navy," but there was a Captain Kane of the HMS Calliope, hit by tropical cyclone in the Pacific in 1889, eventually sailing back to Australia, not to London, and by all accounts in better shape than in Chakotay's version of events. Historical inaccuracies aside, Chakotay's allegory of the chronometer was more apt than ever for the more stricken than usual Voyager in Year of Hell, Part I. At that point, there was barely a bulkhead left unscathed to fly back to the Sol system, and all of time was set against them.
Finding it later in his quarters in Part II, after Chakotay had been kidnapped by the Krenim, the watch never left Janeway's right side. Checking it and empty seat before she engaged on a final, fateful battle, Janeway wore the chronometer until it and the entire timeline stopped ticking in order to begin to tick anew. Now, that's a J/C moment!
Both Janeway's attachment to the watch and Chakotay's "Give Kathryn my best" to Paris on the weapon ship in Part II would tend to suggest that a greater degree of intimacy had developed between the two. We'll never know, however, as all was erased back to "Day 1" and "a bottle of Saint-Émilion".