I hate all of the lying terminal, Pattern Buffer, and shield recharger textures on this level! It took me a good while to notice that "door" to the second uplink chip with all of the confusion of textures!
Good spotting with the hex room secret after the staircase but *ahem* you missed the hex room secret closer to the start - in fact you skipped that whole corridor because it was uninteresting. And if you were wanting plasma batteries, you should have found that one ;). A pistol AND 6, count them 6, batteries await! Remind me to hold those over for Sensori OverLord's vacuum.
On the map there is an indent just -opposite- where the room is, but it is just a ruse. There is a tabbable wall a bit to the right of that indent, and it reveals a switch that opens the door.
What I have only just NOW noticed, going back to check the contents of the room, is that if you stay in that room long enough, the door half-closes, revealing a bloody terminal. And we were being so thorough … but it turns out our map was wrong as well!!
The terminal is upset about our unauthorised access to said fusion batteries, and says that drones have been alerted. But that doesn't sound like something Marathon can do....