I remember reading this quite a while ago, on the K/S archive I think, though I don't know if it was TOS or Reboot.
Spock's pattern was lost in some kind of transporter malfunction. Kirk, quickly becoming depressed, takes to listening to Spock's logs to hear his voice. As such, he discovers that Spock was working on a modification to the transporter, a "backup" device. Sure enough, Spock had built and installed the device and his pattern was recovered, albeit he doesn't know that a significant period of time had passed.
Kirk is very happy to see Spock and, because he now realises how much Spock means to him and is resolved to let Spock know how important he is, tells him that he loves him - but in a brotherly sense. But because Kirk wasn't explicitly clear about the brotherly bit, Spock assumes he means in the romantic sense (as we find out later). For a time everyone is happy and life resumes as normal, with the rest of the crew happy that the two have "gotten together", despite Kirk's protests that yes, he loves Spock, but not like that (the last bit I think was a quote from the fic's description?).
Until someone (either Bones or Uhura) tells Kirk to stop "leading Spock on" - Kirk has apparently been hurting Spock by making what Spock (and the crew) perceives as romantic gestures, but never actually speaking about/acting on the relationship. Disbelieving, Kirk confronts Spock about his feelings outside a bar? on a planet the Enterprise is at with an exchange something like this:
Kirk: Spock, do you love me?
Spock: You know I do
Kirk: But you're actually in love with me, romantically, aren't you?
Spock: ...
Kirk realises he silence is a yes, and being unable to deal, runs off, leaving Spock heartbroken.
The details I can remember after this are sketchy; essentially, Kirk comes to the conclusion that he is in love with Spock and has to convince a defensive Spock that his feelings are genuine. There is a happy ending, I believe.
Sorry for the extremely long description! If anyone could help me with this I would be eternally grateful.