Star Trek: 10 Moments That Confirm J/C (Janeway & Chakotay)

They'd tried the duplicitous, xenophobic imperialist, the holographic barkeep, Q (kinda)… even Mr Paris! Now, for Captain Janeway to have any semblance of a positive romantic relationship, she'd have to have her memories completely rewritten. Nonetheless, despite being based in total, forceful fabrication, Janeway and Jaffen's love affair on Quarra in Workforce, Parts I & II was far from a deception, especially for Jaffen whose identity had always been his own.

In the two-parter, it is Chakotay in disguise (for a while) who goes to seek out the engrammatically altered Janeway. Later, even not knowing who he is beyond 'that guy from earlier from the Central Power Facility,' Janeway feels compelled to come to an injured Chakotay's aid, confirmation enough that the J/C bond persists somewhere deep down in the unconscious.

The deeper moment of connection is at the very end of Workforce, however. Janeway, rescued from her other life, re-enters the bridge, and not without a degree of trepidation in her walk from the turbolift. Most certain is that, from the moment she sits down in near perfect synchronicity in her chair next to Chakotay's, there is no place she'd rather be. "Are you sorry I showed up?" the Commander asks. "Not for a second" is the Captain's unwavering, though longing, reply.