I don't really know if you get them in order in the game (I've done the green route, then the red and lastly the blue one), so here's the info on all 3 of them:
1) The blue route. The 3rd time you go through the portal, just proceed as usual and get ambushed by the nurse bot. In order to get the key you'll need
Qualified Certification. To get it you need to complete the section without loosing a single mash event. Then after the VR test is done, check the book on the lft of the room, then leave and head right to the closed door. Use the certification to open it and get the key from the chest inside:
2) The green route. The 3rd time you go through the portal there'll be a magnet line with the levers. You'll need to get to the end, while using only less than 7 levers, then you'll be able to kick down the box with the key:
3) The red route. The 3rd time you go through the portal, there'll be a puzzle with a copper pipelines. You need to follow the pipeline from the start. If done correctly - you'll get to this area. Go near the black go, but don't enter. Return to the place where the pipe goes into the ground and press the button you usually use to go through the doors:
