There is only one hand that makes sense for the villain, and its not AA or AK, since he wouldve probably raised the flop, and he doesnt have a flush since he isnt 3 betting QdJd preflop. The only hand that makes sense here is 99. Since you raised in the SB, the villain may of thought that 3 betting out of the BB was better than calling with 99 since a 3 bet has an outside chance of folding the two limpers. This is not a bad play since the villain has to call one sb anyways, and both limpers limped from middle position and beyond meaning they both are likely to be very weak(and thus more likely to fold), so investing an extra small bet to 3 bet in this spot with position on the initial raiser, in an attempt to get this pot heads up, with a lot of dead money in the pot, is something a TAG will do.
The plan on the river is this: you have two lines to choose from, bet with the intention of 3 betting or check with the intention of raising. If you think the villain will raise the river if you bet, then the bet/3bet line is the superior strategy IMO.