For two characters that have barely interaction in the last episodes of season 5, there sure is something different there in JJ.
Shopping with Penelope in Exit Wounds is the last time they really speak to each other; when JJ reminds Emily that “Will and [her] make it work” she rolls her eyes, and their relationship just seems to devolve from there.
Emily glues herself to Morgan’s side through the rest of the episode, and it’s not a leap to assume that when “doubling up” JJ goes to Emily (who was not included in the scene, presumably setting up camp), not even realising anything’s different; so when Morgan asks JJ to look after Penelope, it’s not unlikely that she would have swapped out with Morgan. Every scene between JJ and Emily since, they are almost passive aggressive towards each other.
So, then, what happens between The Longest Night and JJ? Because something has shifted, and there’s no denying that Emily knows something, maybe not even consciously. Then, they’re back to how they’ve been since… forever.
During that last scene in the bullpen, Emily is the only one blinking back tears.
And Emily is the first person [JJ thinks of] as she walks off the floor.
There was a post, or tags, or something, by someone, not long after 200, wondering when their relationship had evolved from something that consisted mostly of work and girls’ nights with Garcia, to what was depicted in the episode, (and it’s flashbacks, and then on through season 7), and I think this may have been it.