For the second time you'll see the Guardian (through the pane). Turn left, walk trough the passage and open the door. Take advantage of bridge (#205) destroyed due to explosions and run the only available patch (don't forget about destroying the balls, which are summoning new enemies).
After short walk, you'll encounter Guardian again. He'll be shooting in you direction, so immediately turn right and crawl through the door. You're near the starting place, but on the other side. Jump onto the pipe (#206) proceed in blocked earlier door's direction.
Walk ahead. You'll reach the hall, where somebody closed all door. Move downstairs and look up the gap under the platform (#207). There's a tunnel with cables. Use them to walk on the other side of the complex. Use elevator and travel up.
You should find some armor in the corridor on the left side. On the right you'll find passage to the elevator. Reload your weapons, save the game and use the next cabin to get at the roof.
You must kill Guardian now (#208). He's big and has powerful arsenal of weapons, but the fight won't be especially difficult. Rocket Launcher and Railgun are the best option here. Save the Dark Matter Gun's ammunition for the final battle with Makron. Try to keep at a distance and to run all the time, especially when Guardian will start flying (beware of fire from Jetpack's nozzles). There's plenty of ammunition on the roof, so gather as much as you can. Traditionally, the energy belt will inform you of your enemy's current state (top part of the screen).
When Guardian will become merely memory, push the button (#209) on the most advanced end of the roof. The last signal is now active. Walk into elevator and travel down. Run straight ahead to the portal activated before the moment (#210).