Temple Grounds
The first piece of equipment to find is the Rocket Launcher. The path to get there is still pretty linear.
Hive Chamber B
There is a solid wall blocking the passage forward, but if you shoot the green orbs on the right you'll open a Morph Ball tunnel to duck through.
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.
Hive 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 control panel 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.
Industrial Site
Upon entering, you'll be properly welcomed to Temple Grounds by a short overview. For now, get your Scan Visor ready, as there are plenty of scans in this area in addition to several small skirmishes.
There's another GF Gate Mk VI right as you enter this room. Open it like the one in Hive Chamber A and enter the main area. Get scans of the Green Kralees crawling on the walls above; these won't hurt you unless you bump into them.
There's a large cargo crate dividing the room in half. Use the control panel near the far wall to operate the crane and lift it up and to another area, out of your way for now. This reveals another door with violet hologram, but you still can't do anything with them. Scan the Splinter Cocoons behind the crate before getting too close. If you shoot them or approach then Splinters come out and attack. These creatures actively attack by jumping towards you, but are easily disposed of by a couple of power beam shots. But there must be something wrong if the troopers in the hive let these guys defeat them. When the Splinters are out of the way, follow the ledge to the GF Bridge, scan it (the last GF Security scan), and then cause it to fall into place in the same way you unlocked the gates. Continue along the ledge to the next area.
Collapsed Tunnel
Scan the dead trooper wedged between the rocks on the right. The passage is blocked by a cave in, but you can get through in Morph Ball mode following the tunnel to your left.
Temple Assembly Site
As you enter this area you get a view of the large cargo crate you sent on its way at the Industrial Site. It's left in mid-air. Look above to see a building in the distance held aloft by a huge tower.
Another purple crystal is to the right of the entrance, but you still can't interact with it so 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. There are more Splinter and their hives here so clear them, then scan the control panel near the hologram to lower down the crate you moved earlier. It's lowered part way but the winch gets stuck and it's left dangling. (Ironically, though the crate is indestructible, the system used to move it around is falling apart.) Simply fire a few shots at the sparking part of the line to bring the crate down. You can now jump from the ledge to the top of the crate, then go over to reach the next door.
Dynamo Chamber
Scan the new type of gate in the room. There are three and the first two are open. Now scan the module to the left to open the third and release some Splinters. Opening the third gate will cause the two gates behind you to close and keep you from getting back. When you recover your Space Jump boots you'll be able to jump over them to an upper path, but for now you're stuck on this side.
Communication Area
Follow the passage watching out for Splinter attacks. There are ledges to the side but without the Space Jump you can't reach them. Scan the dead trooper at the end and make a sharp turn to the right. There are more dead troopers here which turn into Dark Troopers when you get close.
Optionally, you can scan the control panel near the troop to turn on the communication array; it will attempt to send out a distress signal, but atmospheric interference will block it.
Trooper Security Station
Upon entering the room, a Growler Class Turret will exterminate several Splinters. This is helpful but when you get close it sets its sights on you. Scan it and then use a charged shot to destroy it. Use the Morph Ball to go through the tunnel to a small chamber on the right. Scan the body there, then scan the control panel to open the door, but damaged systems will cause it to only open a crack before slamming down and attempting to open again. Morph Ball again to the get to the gate and roll under, timing yourself to avoid being damaged when it slams down.
GFMC Compound
The trooper ship landed here. Get a scan of it, then approach to get a cutscene. You activate a recorder to see the captains last log entry. The trooper ship was chasing a Space Pirate frigate to the planet when it was damaged by the atmosphere and forced to land (just as yours was). Unable to call for help because of the unstable atmosphere, the troopers split into two forces, one to repair the ship and another set up a base of operations. There was a surprise attack by Splinters, but these were tougher and a darker color than the ones you've seen. The ship was soon overrun and the first force wiped out; you already know what happened to the second force.
Scan the corpses around the ship to get all but one of the Force One entries. There is a door with a hologram here, but it's emerald rather than violet. You can't do anything with this one either so ignore it for now.
Locate the large yellow crate and use a charge beam to break it open and collect a Missile Launcher. This isn't the one you lost but the troopers aren't going to mind if you borrow theirs.
This triggers a group of Dark Splinters to attack and, just as you saw in the log, they are tougher than the ordinary kind. Get a scan to learn they're being controlled by some kind of parasitic life form that makes them stronger and tougher. So don't mess around; use your Charge Beam and Missiles to take them out quickly.
Board the ship and scan the doors at the stern to access a map station. Now jump out of the hole in its side and onto the ledge. Walk across the ledge and scan the circle on the ground to learn about the Kinetic Orb Cannon. Scan the control panel next to it to turn it on, then Morph Ball and roll in to be fired across the bow of the Tyr onto a ledge on the other side of the room. Jump down to a lower ledge with a Missile door, but before shooting it switch to Morph Ball again and follow the tunnel on the right. There is another ledge there where you can get the last scan for Force One.
Normally when you get a new item there's a lot of backtracking to do to get all the expansions that become available. But even though you've passed several missile doors to get here, the way back is closed until later in the game. Technically, your mission on the planet is done since you've located the troopers and they're beyond any assistance you might render. So now you just have to get your stuff back, wait for the ship to repair itself, and get off of this rock. Your only choice is forward, so get back to the missile door near the Tyr and fire a missile at to unlock it.