Our Xenoblade Chronicles guide features a comprehensive walkthrough and additional info on the endless amount of optional content in the game.
Walkthrough: Colony 6 / Ether Mines
You'll exit the passage near the entrance to Colony 6. Starting from the Watchpoint Junction, your goal is to enter the Ether Mines, via the northwestern path around the bound south from the Junction. You can head for Colony 6 to the south, but the colony is in disarray and cannot be accessed at this time.
Head northwest to access the Splintered Path. Exploring the path will net you plenty of collectables, some of which can be used to complete quests for the Nopon outside Colony 6's entrance. Take the elevator down to the path. Once you exit, you can see the entrance to the mine in the distance. Once you've explored the path to your liking, head into the mine.
As you continue into the mine, you might notice a collectable sitting on a platform that's out of your reach. To get there, hike up the inclined pipes on your left, and leap off the larger pipe branching off of it to reach the item. That's all there's to do here for now.
Head up the staircase to reach the Drainage Control Room, manned by a couple of Nopon. You can purchase items from the merchant, but most importantly, take the time to manage your arts and skills if you haven't already.
The mines are a twisted maze of corridors. It's not terribly hard to get to the goal, but there are lots of opportunities to mine ether deposits, nab collectables, and otherwise get turned around. The cave is littered with Mechon, so don't forget to Enchant Reyn and Sharla at the start of each fight to move things along. There's a path that heads far south, leading to a secret area, Glowmoss Lake. The main attraction here? For now, the most you'll get out of visiting the lake is a sizable chunk of EXP. The UM in the area is likely too high level for your team at the moment, but there are a few collectables strewn about, if you're on the hunt.
When you've satisfied your need for exploration, head for the goal at Test Pit 3. After the cutscene, take out the Mechon on the platform, and get ready to meet a new ally. After the introductions are made, it's time to head deeper into the mine. There is a Heart-to-Heart location nearby, but not much else in the immediate vicinity.
Head south and you'll reach the Central Terminal. This is where navigation gets quite tricky. Though your goal is marked on the map, you'll have to activate a device in order to use the elevator located at said goal.
For a point of reference, I'll provide directions from that marker. Return up the path that led you there and take a right, heading northeast. Run up the small staircase and take another right when you reach the next fork in the path. Drop into the gap in the floor and turn right again, heading south this time. Take a quick left, and follow the path northeast until you reach Observation Point. Head down the staircase to your right, and activate the switch to open the gate that was previously locked. Backtrack to the goal and you'll enter the Central Pit.
There is an apparent mistake in Special Lever 2 for Regbuilding Colony 6. It says defeat Earth Nebula at Sap Cave. I was never able to find a Sap Cave, but I was able to defeat Caris Nebula at the brog lake just before you get to Nopon Arch.