Mako loses himself in work those 3 years. Korra doesn't reply to his letters but apparently she doesn't reply to the others either. He wants to know how she is, how she spends her days, whether she's getting better, only he can't work out how to ask when she refuses to answer.
The silence unnerves him so he works.
Several months later Tenzin says that Korra is improving. Mako refrains from taking leave to visit her there because he is the responsible one. Always was. (Always will be). So he waits.
He worries that he might forget her and spends the nights remembering; everything he has ever heard her say, her facial expressions, the way she fights, everything. But time still passes far too slowly. (He wonders whether she tortures herself like this and cannot decide if he wants her to be in this pain with him or not).
He gets promoted, or demoted depending on your view. Babysitting Prince Wu is not what he envisioned (it was blue eyes and a fierce smile) but it's a welcome change. Going to Ba Sing Se with Wu is not something he plans to do and once Korra arrives (soon) she'll find a way of stopping it. She always does.
Tonraq steps off the ship and his stomach drops to the centre of the Earth when they realise Korra is gone.
(Please come soon. Please come soon. Please come soon. Even if we aren't the same, just come home. Let me know you're ok. Please. Please. Please.)
So he waits.