MP1 is 14/7/2.2 over 444 hands
CO is 12/8/3.2 with a 5% 3bet

I wasn't really sure whether or not I should be 4betting here.

Full Tilt Poker $0.10/$0.25 No Limit Hold'em - 9 players
The Official 2+2 Hand Converter Powered By DeucesCracked.com

UTG: $13.56
UTG+1: $35.89
UTG+2: $25.32
MP1: $28.68
MP2: $26.81
CO: $32.57
BTN: $9.08
Hero (SB): $25.00
BB: $25.00

Pre Flop: ($0.35) Hero is SB with Q Q
3 folds, MP1 raises to $0.75, 1 fold, CO raises to $2, 1 fold, Hero calls $1.90, 1 fold, MP1 calls $1.25

Flop: ($6.25) 2 6 8 (3 players)
Hero checks, MP1 checks, CO checks

Turn: ($6.25) J (3 players)
Hero bets $3.50, MP1 calls $3.50, CO folds

River: ($13.25) 5 (2 players)
Hero bets $5.25, MP1 raises to $14.75, Hero requests TIME, Hero folds

I'm pretty sure I played this poorly. What line should I have taken?

i really think preflop is fine, anyone wants to 4bet/shove pre?

as played B/F B/F C/F

If you're ready to get 5bet for your whole stack, then you can 4bet. I think flatting the 3bet is fine.

Personall, I think your overall line is fine. Bet bigger on the turn and river for value, to worsen odds for chasing a draw and to improve FE. Reraise shove the river. I think you're ahead here. He may have sucked out a flush but if so you got your money in good.

If this advice is stupid, I'm sure someone will let me know.

I think checking the river scare card against a thinking player to induce is better than bet/folding but either way is fine other than that your line is completely fine and i dont think, after he raises, you are ever ahead vs this type of player so folding is correct

Your play preflop and on the flop is OK. Playing QQ from OOP in a 3-bet pot is a difficult situation to be in.

On the turn I believe you need to bet more than $3.50 (into a $6.25 pot). With 2 flush draws on board there are many, many cards that you do not want to see on the river besides an Ace or a King. This is a decent sized pot and I would try to take it down now with what is most likely the best hand. Hence I would be betting something around $5 on the turn.

The river card is one that you didn't want to see. Given MP1's postflop play there is a chance you were just outdrawn. Before I put any money into the pot on the river I would decide how I would respond to a raise from him. And if you are going to fold to a significant raise then betting out is a major mistake.

I would fold pre TBH, and here's why...

you have a 14/7 setminer open in MP, and he gets 3bet by a nitty setminer in LP. You have QQ OOP. A 12/8 does not 3bet JJ pre, so you're either up against AK, or KK/AA. So either, he has two overcards, and you don't get any value out of your pair, or he hits an A/K and you have to fold, or you have an overpair, and get stacked by KK/AA.
edit: And setmining OOP in a 3bet pot is just plain bad, so you can't call for set value.

I would just stay away from 3bet pots OOP with QQ... this is a leak I've only very recently plugged.