Wait, you have Level 99 in all roles and you can't beat him? That's not possible. We ARE talking about the three Bahamuts, right? You should wipe the floor with him.
If my hunch is correct, you need to develop the other roles as well. Tghe stat boosts you receive are not locked to the role the boost was achieved. If the non-combat Role emdic gives you a strength boost, the Commander has that boost as well. The same goes for HP. It flows into the character, not into the specific role.
Of course, skills are role exclusive. Only medics can cast cure.
Either way, what's your problem with the fight? I can'T help you if you don't tell us what's going on.
The best thing I can advise you to do is doing sidequests to collect fragments, so all the other roles can be improved. And bring a Sentinel-Monster with you. I like the turtle-monster from Achylte Steppe, it's there during rainstorms at the swamp area. It's missing the healing sphere ability, however, so you might want to infuse another monster into it, to receive it. Either way, Sentinels reduce the enemy's damage output. And if you bought any DLC and requiem is one of it: I consider Commander Lightning to be a game breaker. (Five Stars on Final Boss on my first try, on normal. Without even trying. That's NOT funny.)
How do you know it's the last boss? Is it three bahamuts on a platform? And where do you fail?
You made it past proto-behemoth, who is much stronger than the final boss. So you are strong enough, just need a better strategy. Here's a basic strategy based on my method that works for almost all non-DLC enemies and bosses
Take out the first two bahamuts one at a time. Many people suggest bringing the one down to low health, killing the other, then the first. Apparently they respawn after some time, but I've never seen it happen. Then the black bahamut. He hits you with a lotta status ailments at the start. I just use 2 medics to quickly fix everyone up, but you can also use an item for it. Get a sab to poison bahamut, and deshell&deprotect if you can (you can also wait for him to be staggered and more susceptible before the deshell/-protect if you dont mind losing a few seconds of smackdown time). If both Serah and Noel are sabs at the same time, it goes much faster. (most people also suggest imperil, and then en-spell yourself with a syn) Tri-disaster (rav-rav-rav) till high-stagger, then cerberus (com-com-com) till he's dead. Apparently he has some super-powerful attack that he uses if you take too long. So try focussing more on attack than defense.
So you need a rav, com and med monster. com - rav - rav rav - rav - rav com - com - com-x sab - sab - med/rav med - sab/sent/com - med rav - com - med
Preferably ones with good Feral Links that buff you. If you got the requiem DLC and dont mind major endgame spoilers, get Lightning (com). She'll make it easy. But you'll have to run through Academia 500 again.
I'd recommend RAV/COM/SYN for your monsters; at max Crystarium Noel and Serah should be plenty good enough for MEDs.
Taking out Amber and Garnet as close to each other as possible buys you more time against Jet before he brings them back. Since Jet is the part you're having trouble with, I'd recommend going to the trouble of doing this.
Even if you go elsewhere to recruit monsters, you don't need to go through all of Academia 500 again. If you exit to the Historia Crux from the point right before the final boss sequence, that's where you'll be when you come back.
Possibly the easiest highly effective pack of monsters to use here is Dragoon/Cloudburst/Yakshini. Dragoon is quite powerful with minimal effort (just max its level), and the other two have awesome buffing Links that will make your life easier.