Okay, I'm going to call it right nowClick to see Spoiler:Mahone is calling Mr. Kim to Panama with the intention of killing him. In the preview we see Mr. Kim about to shoot someone (Lincoln maybe) and then we hear a gun shot. I think it's Mahone shooting Mr. Kim.
I guess SONA won't be explained until next season. But there is still 45 minutes to go so maybe we'll find out more before the finale is over.
ETA: I was a little bit wrong. Right about theClick to see Spoiler:doublecross, but since Mahone's in custody he won't be shooting Kim. Maybe Sarah shoots him?