After you collect the Atlas, all hell breaks loose. Your positions will be attacked by the Trinity soldiers. Try to use all available covers and do not remain in one spot for too long, or you will be peppered with grenades. You can deal with the attackers by shooting at the containers with Greek fire. The liquid will set them on fire.
After you defeat the first wave, walk over to the next chamber, where you are attacked by more enemies. They come armed with weapons with laser rangefinders and they will easily spot you, so you need to watch out here. Try to disappear from their sight and climb onto one of the elevations, from where it is easier to attack them.