After spending far too many timelines cracking mountains with nothing to guide my search, I am making this guide to help anyone else who is looking for the Distant Friends achievement.
Other Into the Breach Guides:
1: Recommended Set Up
The special glowing beacon, when spawning in mountains or ice, can spawn inside of pre-damaged/cracked tiles. This means that at the beginning of every battle, just look at every square. You may see a beacon glowing right from the start! You just have to know what to look for. See section 2 for many examples of beacons in mountains and section 4 for an example of a beacon in ice so you know what exactly to look for.
In fact, the vast majority of beacons you will probably encounter are found in these instances of pre-damaged/cracked mountain and ice locations!!!
1A. Set the game difficulty to EASY mode. You are going to be wasting a lot of time and firepower cracking mountains, and there's no way Normal or Hard will give you the luxury of free actions to break open mountains. Not only do you need to crack dozens if not hundreds of mountains to find what you are looking for, but once you crack it, you need to then destroy it and move a unit to pick up a drop.
1B. Bring Mechs with lots of firepower, and AOE firepower as well. Science types that deal no direct damage are of no help here. Mechs like the Mirror Mech that can hit two distant mountains at the same time or the Artillery Mech that deals damage all around the target square are your best friends for this hunt.
1C. Once you have your squad, it's mountain cracking time. Control the Vek with as few moves and effort spent as possible (this is why you want to be on easy mode). Then spend all extra actions you have left over using your Mechs to attack mountains wherever you see them. Once you crack a mountain (1 damage) you should be able to see the glow right away. If you don't, move on to the next mountain. Be prepared for a long grind, I spent at least 5, 10, or maybe even 15 timelines focused just on cracking mountains, staying alive so I didn't get a game over, and not much else.
2: Screenshot Walkthrough of What You Are Looking For
2A. The glow you are looking for in a mountain, note the bottom left mountain has a yellow dot inside.
2B. Pilot makes a remark, and you see a small beacon on the square now.
2C. Move a Mech to pick up the small beacon.
2D. Special FTL pod will arrive. Thankfully you only need to protect it, you don't have to hustle over and actually pick it up during the mission.
2E. Opening the special FTL themed pod...
2F. Earning the achievement.
3: Other Details
3A. There appears to be three total special pilots. From what I have gathered, they are each tied to a specific zone. Mantis in Grassland, Rockman in Acidland, and Zoltan in Desertland. Striked out statement proven to be false. You only need one to unlock the achievement.
3B. Each Pilot has very unique stats, if I ever acquire them all maybe I'll update the guide to show them all.
3C. As far as I can tell, there is no hidden pilot in the final zone, nor in the Iceland zone. I am very much NOT 100% certain about the Iceland zone not having a pilot though, I just have not found any evidence yet to support that zone having a pilot. Striked out statement proven to be false.
4: Edits / Updates / Corrections
4A. Pods can be found in the Ice (Pinnacle) Zone. In fact they can be found here buried under the ice as well. So get cracking with those AOE attacks!
4B. As noted above, beacons are confirmed to be found inside of mountain squares and also potentially now in frozen water/ice squares.
4C. Specific special FTL aliens are not linked to a specific zone. Here is the Mantis being found in the Acid/Detrius zone.
4D. Special beacons can be found on any difficulty mode, including hard. But good luck having the spare time and resources to spend searching and acquiring them on hard!
4E. Special beacons, when spawning in mountains or ice, can spawn inside undamaged tiles or pre-damaged tiles. This means that at the beginning of every battle, just look at every square. You may see a beacon glowing right from the start! You just have to know what to look for.
Bonus: Alien Portraits and Unique Stats
Using the above strategies and tactics, I was able to acquire every FTL alien pilot with just a few hours dedicated effort. So here are all the portraits of the secret pilots as well as their stats!