Hive Chamber C
This room contains another squad of Dark Troopers. Deal with them as you wish, then go through the door behind the crates on the far wall.
Save Station
Use the Save Station to restore your energy, but not your ammunition. Go back and continue to the next room.
Hive Transport Area
After entering this room, scan the Interface Module to activate the elevator. Step into the hologram to activate it and finally exit the hive. The room is connected to the same room you used to access the hive earlier, but you still can't unlock the Violet door, so head through the other door towards the Federation base.
Federation Base
Upon entering this area, you'll be properly welcomed to Temple Grounds. For now, get your Scan Visor ready, as there's plenty of scans in this area outside of several small skirmishes.
Industrial Site
There's another GF Gate Mk VI right as you enter this room. Open it like the one in Hive Chamber A. Now that the gate isn't blocking you, there's a large cargo crate dividing the room in half. Use the nearby Module to lift it up and out of your way with the winch system above you before it gets carried to another area of the encampment. Once that's done, begin hopping up the ledges on the other side of the room. There are several Splinter Hives on the walls of the ledges; scan them without getting too close, as if you approach them, a Splinter will pop out. These creatures actively attack by jumping towards you, but are easily disposed of by a couple of power beam shots. The Green Kralees ahead follow a preset path and don't attack, so they pose no threat. Once you get to the GF Bridge, scan it for another Research entry and then cause it to fall into place in the same way you unlocked the gates.
Collapsed Tunnel
Scan the dead marine wedged between the rocks on the right to get a Lore entry. Go through the Morph Ball tunnel to your left to reach the door.
Temple Assembly Site
Yet another crystal is to the right of the entrance, but don't worry about it for now. There is also a missile door and a violet hologram door that you can't use for now, so scan the module near the hologram to lower down the crate you moved earlier. When the winch gets jammed, simply fire a few shots at the sparking part of the line to bring the crate down. Cross this to reach the next door.
Dynamo Chamber
Scan the new type of gate in the room. Unlike the other gates, all you have to do is scan the module to the left to open it; however, this will cause two gates to lower and seal off the lower path. You'll come back to those two gates later in the game, but right now, continue to move forward.
Communication Area
A couple of Splinters and Dark Troopers are lurking in this room. Other than that, the dead trooper on the floor will give you a Lore entry. If you scan the Interface, the array will attempt to send out a distress signal, but atmospheric interference will block it. Continue onwards.
Trooper Security Station
Upon entering the room, a Growler turret will exterminate several Splinters before setting its sights on you. Scan it and then use a charged shot to destroy it. Use the Morph Ball to go through the tunnel and scan the Interface, which will open the door, but damaged systems will cause it to only open a crack before slamming down and attempting to open again. Scan the body in the station for a Lore entry, then roll through the tunnel. Use the Morph Ball to head through the gate, timing yourself to avoid being damaged when it slams down, to get to the door.
GFMC Compound
This room contains a multitude of scans. Upon entering, scan GFS Tyr, then approach the console in front of the ship. Scan the corpse leaning on it before you get too close for some Lore, then walk up to the console to discover the fate of the marines. Blow up the large yellow crate to regain your Missile Launcher, although you can only carry 5 missiles now. To celebrate, a group of Dark Splinters will enter the area; get their scan and then shoot them up. Explore the rest of the room, as another 5 Lore entries are carried by marine corpses scattered throughout the room. Once you get them, board the ship and scan the doors at the stern to access a map station, then jump out of the hole in its side and onto the ledge. Walk across the ledge and scan both the Interface Module and the Kinetic Orb Cannon. Get into your Morph Ball and roll into the hologram to get fired to another ledge. Fire a missile at the red door to unlock it.