Based on this tumblr post.
Spock, as we know, is biligual, and besides speaking perfect english, Jim notices he sometimes will mutter something under his breath in Vulcan. Jim figures it's probably just Spock thinking out loud or cursing to himself or something. Then, Jim secretly learns Vulcan with the intent of surprising Spock with it, and it turns out that it’s a constant flow of praise or dirty talking. Eventually, Spock figures out he knows Vulcan somehow (maybe overhears him speaking with a diplomat?) and confronts him.
Bonus points if:
They're not together to start out with.
It's fairly long, 5k words at least would be preferable
Jim formerly believed Spock had no interest in him and is shocked when he understands him
The reason Jim keeps it a secret is that he thinks Spock would stop if he knew
After they figure it out Spock starts to use it for talking dirty and getting Jim flustered and/or aroused in public places.
There's a scene where Uhura overhears it (no Uhura bashing).
They think they're being inconspicuous and McCoy confronts them about being obviously all over each other.
It's TOS but AOS is still fine if you prefer
Characters: McCoy, Uhura