Ok krum2000, I want to give you props for coming on and asking for help. I won't assume that I know everything wrong with your game based on one hand that you're admitting you had a problem with.

You're a big stack at the beginning of this hand. You might have been running the table a bit and known full well what your effect on the table was, and what would happen when you raised. You said in your follow-up post that you wanted to take the pot right there, and if that's true, you probably knew what you were doing since almost everybody folded.

Like fnord implied, 99 is a fun hand to play poker with. If you can play post-flop, you can make a nice pot with this hand every so often, so it's not the most attractive candidate for stealing blinds/limps.. But you chose to try and steal with it, and you almost did it. Not as horrible of a play as it's been made out to be, but a play that's suited better to short stack moves (at least at 25NL). You don't want to flirt with coinflip scenarios (or worse) this voluntarily when you don't need to.

As far as the flop goes, I think you probably knew it was a mistake before you clicked the check button. Might make this kind of mistake every so often. Hopefully less-so over time. Might get rewarded for making this mistake every so often. You are not a retard. This is a plenty common mistake, and slowplaying a made hand against an underdog can be a temptation. Just remember that you are sacrificing opportunities to get information when you start playing tricky/slow, so you better have a tighter read on your opp when you do (i.e. - know that he isn't drawing), or it can bite you in the ass as it did here.

You made the small turn bet for 'safety' reasons, but you can see how that can invite more danger. Most players at 25NL aren't gonna bet (or-reraise) a nut flush when they make it with cards left to come. The size of your bet is smaller than what you raised preflop, less than half the pot, and typically shows fear of the board. You're giving him fair odds to keep drawing (which you would want to still be considering...don't just think flush) plus the opportunity to represent the flush depending on what you do on the river (he'll be watching, to get more meaning from your turn bet).

And besides giving the strength of your hand away (it doesn't matter that you're giving it to a worse hand), your turn bet doesn't necessarily buy you a lot of info. Say he made the nut flush on the turn. Even if he has a superman read on you and knows you have a set of 9's, you think he'll re-raise the turn to protect? Your chances of making full on the river are not super threatening and he'd want to keep you in the hand more often than not. You'll get the same call you did in this hand many times. This way he also keeps from looking too strong so he can try for a couple extra bets on the river when the board doesn't pair and he knows he has the immortal nuts. I think you're more likely to get raised by a hand that's still drawing or a hand that was made on the flop. Really, he should have tried for this with his straight anyway, and since he didn't ever reraise you, he wasn't sure if he had been drawing dead which makes his calls 10x worse than your bets if it makes you feel better about this hand. The main thing wrong with your betting was the lack thereof or the lack in size.

The river bet is bigger than the turn most of the time, so if you're losing to a flush already you don't want to get smacked for one more round at your opponents chosen price. It's time to find out now. It cost you $6 for the turn and river combined to play it the way you did (going into a ~$5 pot after checking the flop) and gave him the opportunity to draw, bluff and win. Two of which he did, and a different player could have easily check-raised your turn or river bet with or without the goods. Consider what would happen if you bet that same $6 or so on the turn. A pair of eights with a straight draw will think a little harder before following you to showdown with 3 hearts and overcards on the board. You'll make it a thin call for lots of hands and maybe even get some players to fold a baby flush (unless you're too easy to read because they know you usually slowplay bigger hands). A high or nut flush will re-raise you, or call and bet the river. You fold to major aggression at this point, and oh well, nh opp. But a lot of times you'll take it on the turn. Remember that your 'safety bet' should be enough to help you know when you're beat by telling your opp you think you're strong, not vice versa.