The hive is saved but humans and doctor Eisenberg in particular try to flee. Worse than that, they took the Empress with them. Stop them at all costs.
After a few steps you will appear in a hall with two turrets on a ground floor and a soldier on the upper floor. Get rid of the soldier first, then jump down and destroy turrets trying to stay in their blind spots.
Move forward, turn left and kill a human ahead. Near the spot where he was standing there is a damaged grille. Smash it and jump down, then jump down again. One guard will spot you this instant, two more will charge at you, so you will have to be really quick. When you're done, smash the sentry gun access panel and a circuit box to the right. They are pretty big, not hard to spot.
This will open double doors and you will be attacked by two humans. Careful, one of them has a minigun! Either pounce on them or try to lure them out. You need to drop down but there are two guards who already know about your presence. Either drop down near them and kill them as fast as possible or drop down behind the vehicle and try to lure them to you.
Enter double doors behind the vehicle and smash a sentry gun panel. Then go back and smash the circuit box in front of double doors. Inside there is another sentry gun panel to be smashed.
Turn left. You will face a guard, another one is behind a pillar and will come out as soon as you're compromised. One more guard is patrolling somewhere nearby. Despite there are many corridors and some elevators, these are all dead ends. You have to break a grille to enter a technical floor. It's near the ceiling and highlighted in red. There enter the vent, drop down, break the damaged grille and drop down again. Nothing you haven't done before.
You destination here is a huge fan which has to be stopped first. See three boxes on the walls that lead to the fan? Smash them. As the fan stops, climb up and kill two guards. There is no way no know where those two stand in advance. You have to save your game, climb up and see if you've chosen a good spot to emerge or not. Most likely, a synthet will run to you as well, so get ready to face more foes.
From there you can proceed straight forward to see a vehicle leaving the place (most likely, with Eisenberg) and get killed by humans and turrets. Or better turn left, smash the grille and jump down. Follow the vent and emerge after smashing another grille.
You're in a room with big yellow tanks. One guard will start shooting at you this instant. Another one is on higher ground and requires careful approach. At least there are lots of spots to hide from enemies. At some point one guard will spawn on the ground floor. Once you get rid of the guard above, smash the circuit box. Go to the hole appeared after the explosion. Turn either left or right, both ways lead to the same corridor.
Alright, you've been here before. You're in the beginning of the level, but now you're out of turrets' reach, so turn right, kill all humans and destroy turrets. Destroy sentry gun panel and head back.
Upon exiting stone tunnels you can turn left and go to where the vehicle disappeared. Another dead end. Climb up and looks for a circuit box near double doors. Smash it and enter the doors.
There will be a guard straight ahead. If you pounce on him, you will get shot by two enemies from the left tunnel, so it might be wise to lure the guard first. After that there is only one way – to the left. But be careful – there is a guard with a minigun ahead and it's difficult to lure him out.
You know what to do. Smash the circuit box and go through the doors. Two guards ahead will charge at you as soon as the door opens, so be careful. The next part is harder. First of all, you will be attacked by a synthet which has more health and is not highlighted. Try to deal with him quick because two guards will attack from the left tunnel. Luckily, there are lots of boxes to hide behind, but if you won't get rid of a synthet quick, they won't help you.
Now you might be extremely confused. Where to go? All doors are shut and there are no vents to crawl into. Actually, the solution is quite simple. Get as close as possible to one of the closed doors to end the level.