Keep moving forward. Turn right and use a nearby ladder in order to get to the lower level. You will have to approach a smaller assembly line. As you've probably suspected, you'll have to solve a new riddle here. I wouldn't recommend saving your game here, because this may disrupt your progress. Make sure that you're standing near the assembly line. Wait for the machinery to perform at least one full cycle.
Now you will have to wait for one of the crates to show up here. Wait for the crate to be placed on the assembly line. Enter it as soon as possible (screen). Once you're standing inside an opened crate, use a reverse time feature. If you've done everything correctly, the power bar will begin lowering its value very slowly. Otherwise you will have to repeat all of these actions.
Make sure that you're not moving once you're inside a closed crate. Allow the machinery to move it back to the previous room. Observe the power bar. You'll have to act quickly once you're on the other side. Otherwise you would be trapped inside the crate and you would have to wait for the machinery to return it to original position. You will find yourself inside a new room of the factory.
One of the engineers in this room, however you should be able to surprise him. Once he's gone, head on to the stairs. Keep moving forward. Ignore some of the nearby tanks. You won't have to do anything out of the ordinary here. Enter a new room (screen). You will have to wait for the game to unlock a new passageway for you. Save your game here.
You are moving towards a large room. Your first concern should be an opponent armed with an energy shield (screen). You've got two choices here. You can try and weaken his shield with a Hell-Fire or you could move back and try to eliminate him from a larger distance. Either way, he has to die. Once this is done, take his weapon and get ready, because there are more enemy soldiers in this area.
Try making a few steps forward. You will have to eliminate a few snipers from here. Make sure that you're using your map to find them. Once they're gone, move closer to the balustrade and check lower floors for additional troops.
Make sure that you've killed all enemy soldiers. Head on to your left. You shouldn't encounter any soldiers right away, but eventually you'll come across two other snipers (screen). Kill them with your crossbow and by activating a slow-motion feature. Keep moving forward. Now you will have to deal with a small group of enemy soldiers. Use the Hell-Fire machine gun to get rid of them.