When you reach this research institute, you are likely on a mission from Sidorovich to recover research documents. The mission involves breaking into a military base to steal these documents.
There are three major sections in the Agropom Research Institute.
When you first approach Agropom, you will see a Stalker calling for help. He says that mole's group is under attack, and asks you to help out. Advance towards the first location, and a cutscene will start showing the overview of the battle (you can skip the cutscene by deviating onto the left path before heading to the entrance.)
In the main factory, the loners and military are engaged in combat with each other. When you help defeat the first wave that in firing sights from the entrance, you will receive an announcement that Mole is in trouble and needs to be rescued. He is in the south of the factory, although you won't have as much support from other Stalkers when rescuing Mole.
After you save mole, you can speak with him. He will bring you to a secret tunnel to an underground section, where Strelok kept his stash.
When you enter the underground section, you should have some data in the PDA that shows the route you should take. While you could attempt a more direct path, it may either be blocked or covered by dangerous anomalies.
The underground section first contains bandits. There are about eight of them, and they will generally attack from behind cover.
When you follow the path, you should reach a long curved room. This is occupied by a bloodsucker, which is an invisible enemy which can be spotted by visual distortions. If it detects you, you may be able to return to where you entered as it will not exit the long curved corridor.
After this corridor will be two remaining soldiers. They may be alerted if you engaged the bloodsucker or used a loud weapon near them.
Head to the map marker leading to Strelok's stash. You can find the objective item, Strelok's flash drive, found behind one of the boards. Elsewhere in the room is a Fast-shooting AKM 74/2, and a Stalker Suit (which provides nightvision).
You may now exit the underground. If you follow the minimap arrow, you will encounter a few more soldiers, before reaching the exit corridor. Save the game here.
When you pass the first section of the exit corridor, a loud scream behind you signals the approach of a Controller. If you can't defeat it, head to the end and climb the exit. If you choose to fight, take cover when you hear the high-pitched noise, and engage it with your weapon of choice.
Agropom military base
When you emerge from the underground, you will be inside the military base. You only need to grab one item, the "Document Case" in the top floor of the main building. In some versions of the game, saving and reloading (including the level change save) while in the base may cause the soldiers to become alert.
Return to Garbage
There are three enemies that will intercept you as you leave the institute, just before the transition. You can handle them as desired.
When you return to Garbage, you are likely to be called to assist in defending the Stalker base against additional bandits.
When you have the document case and returned to Garbage, you can head north to the Bar to receive the next mission.