Once all his best relationships faded into the past, Chakotay became a free agent, and his spotlight episodes were uniformly episode-of-the-week endeavors. Though fans still liked to think of the possible romance with Janeway, Chakotay stayed on the shelf until the end of the series, when he hooked up with Seven, for all the reasons that kept him there all that time.
But his great romance was "Unforgettable," a heartbreaking experience with someone who predictably could never remain a permanent fixture of his life, not just because she was from a random alien species the ship was going to move on from soon enough, but because she couldn't remember him, and was a secret agent besides...Janeway had her own relationship almost exactly like this, too, but Chakotay had the best one-off experience of this kind in the series. It has no lasting consequences and means nothing to the continuing saga of the crew, but it's arguably the best episode for Chakotay in the last four seasons, a capsule of the frustrations he experienced on a regular basis with the pesky Seska in the first two.
franchise * series * essential * character
Memory Alpha summary.