Welcome to the THRESHOLD 100% achievements guide! Obviously, play through the game once first and then come back here, there are major spoilers and at the end of this guide I will theorize about exactly what do the numbers mean, what happened to Ni, and why are there so many animal carcasses!

"You met your new partner."
This one is unmissable, simply go through Mo's process of introducing you to the job and what you need to do.

"You consumed 15 Air Cans."
This one is possible to miss, but very hard to do so. Just eat a bunch of glass and inhale a lot of air. If you're having trouble getting lots of air cans, you can sit by the ticket producer (as it produces tickets every time a train car goes by) and farm up a bunch.

"You flushed a corpse down the Recycler."
Eventually the train will completely stop, progress the story as normal but after you start the train again go down into the river to the filer. There should be single fish, collect it with your bucket and bring it to the recycler, then simply flush it down.

"You crushed all kinds of things."
You need to recycle the following five substances.
1. White Goo
2. Gravel
3. Water
4. Waste
5. Fish
I already explained how to get the fish and the white goo is explained by Mo. You can pick up gravel pretty much anywhere on the ground and the water is obviously collected from the stream. In order to recycle the waste you need to desecrate Ni's grave (the pile of gravel in the corner, by where the water comes from).
Once you do this it'll unveil a red key in his hand, use this on the outhouse seat and inside will be waste for you to recycle.
If you're having trouble with this achievement, make sure you're collecting a full bucket of each of the five substances to recycle.

"You actively took part in the destruction of the Border Post."
Along the path to and from the elevator is a hole in the wall with two planks. Remove both of the planks and you'll have took your part.

"You cleaned and repaired everything in the Border Post."
After you collect all the planks that Mo asked you to collect, bring him to the pile. He should make a couple comments on it and then ask you to repair the window. Do so and you'll be deemed a good dog.

"You found all the Air Cans scattered around the Border Post."
There are many free air cans scattered about, here's a guide I made that can help.
https://psteamcommunity.yuanyoumao.com/sharedfiles/filedetails/?id=3369438081

"You asked all the questions to the capital."
There are many question to ask the capital, here's a guide I made that can help.
https://psteamcommunity.yuanyoumao.com/sharedfiles/filedetails/?id=3370386653

"You didn't ask any questions to the Capital."
Finish the game without ever going into the capital building unless you are required to.

"Capital Chambers communication system has been terminated."
After you discover the trains contents from the observatory, Mo will report you to the capital building. If you've seen all the bloody messages from Ni (on top of the shed, behind the boxes in Building Two, and in the observatory), you should be able to desecrate Ni's grave once more and this time it'll reveal his mouth and black whistle.
Once you speed up the train again and are called into the capital building, use the black whistle inside.

"The Train is going back."
As the THRESHOLD begins, if you haven't gotten it, go to Ni's grave and desecrate it to get the black whistle. Use that whistle on the train enough times until it begins going backward.
If you're having trouble keeping your air, I recommend collecting a bunch of tickets before the capital calls you in and takes your air cans, use those tickets to produce many air cans and leave them on the ground. Then come back to them once the capital releases you.

"Duckey has been saved from the Threshold."
Remember that hole in the wall with the planks? Go back to it, but instead of removing the planks, stare into the darkness. After looking in for a bit, a duck should pop out. Interact with the duck enough until you are allowed to pick it up. Once you can pick it up, bring it with you to the next ending achievement.

"You fled."
During the THRESHOLD many, many bodies will be piling up. Wait for enough of them to pile up to where the trees collapse. Climb up the tree leaning on Building One and scale the mountain, this should then eventually trigger a small cutscene of you looking back and forth and then fleeing.

The Bond was not broken.
Once again, get to the THRESHOLD, but this time don't do anything. Let yourself run out of oxygen and you will have hemorrhaged.

You have now (presumably) fully completed THRESHOLD, good job! Now time for my thoughts, as promised.

Firstly, I do follow the theory that the numbers are some sort of counter to how many animal are consumed or slaughtered in the country. My idea is that the overall number is how many animal are in captivity or slaughter farms, and the fallen number is how many are killed each day. I'm unsure on this, and so far there is no straight answer.

Second, what happened to Ni? Well, obviously he died, but I don't think Mo killed him. If you stare at the rope hanging from the observatory you get a small jumpscare of what appears to be a Yellow Clerk hanging. This is presumably Ni, assumingly after he discovered what was in the train. He clearly couldn't take it and hung himself. Then Mo buries him, they compensate the family, but obviously don't talk about what he saw or exactly how he died.

Third, the massive amount of animal carcasses. I suppose this just ties back to the first question about what the numbers mean and how many animals the country you selected slaughters.

Now, a final question I have for you: "Where did the black whistle come from? Did Ni make it after what he saw in the train or was his job previously slowing the train down if it got too fast?"