It seems none of the other guides describe properly how to complete the ending in the best possible way, only in other forms. While it is possible to beat this game as soon as possible. There is, in fact, a best ending and I'll tell you how to do it. You can beat this game in any order you like when you've reached the ending point of the game. For me, I've elected to beat this game in the order of how the short story ended. Where, Gorrister, Benny, Nimdok and Ellen dies. Ted survived. Instead of being transformed into an alien-looking jelly creature, Ted is going to take his revenge on AM by shutting him down and sparing the lunar colony for humanity! At the sacrifice of his life.

*Note - You can do these in any order too, just make sure you do them and try not to piss them off before you do.

So, here's what you do:

Invoke the Totem of Clarity, which is the same hand mirror you picked up from the vat of mercury in Nimdok's scenario. Use that on the Superego.
Invoke the Totem of Forgiveness, which is the open book and it is something the Russian and Chinese counterparts advised you to do only.

Well, screw their advice because next you Invoke the Totem of Compassion to the ID. Which is the doll you've made for the child in Benny's scenario.

When you're asked for the Totem of Entropy, refuse it at first, do not invoke or give it away right off the bat. Given that you haven't given it away to gray demon you first meet. The second chance you get, however, you'd Invoke the Totem of Entropy.

This should trigger the best ending where whomever you picked last will say something along the lines of "I will keep the machines in place." which is what you want. You could easily screw this up and the character may say something like "I keep the machines in place, most of the time." which means that you did something wrong.