This guide consists of several chapters, as the game itself is. There are 3 choices in the game, as well as one series of choices, each of them is numbered on the map. It is recommended to save at each part if you don't want to restart anew each time.
I will explain the routes, but leave the actual decisions as spoilers for those who want only a bit of help.

Here the plot splits for the first time. If you choose to let Bell go away, then you follow red path which ends the game. If you choose to stop Bell, then you continue on the black path. Red path earns you an Unchanging achievement.

This is the second choice in the game, however, at the start you have only yellow route choice: to write nothing. Second route unlocks when you get both yellow endings. Then you will be able to write about Bell. If you save the game at this point and reload when second branch is opened, you will be able to choose it, you won't have to start the game from the beginning.
Even though there is a choice, there are only a few different lines at this point, and the actual difference will be noticeable only after 3rd choice.

Here you can get two achievements. Both of them are on the yellow route, and once you claim them, you can get to the green route.
To get Clear Sky(left route) you'll have to tell Bell she's your girlfriend.
To get Memory Puzzle (right route) you'll have to tell Bell she's your irreplaceable family.
If you get on the green route, this choice doesn't matter, and the only difference it makes is whether Bell drops the bell or not.

If you unlocked both yellow endings and then went green route at part 2, then you get here. The first time you can see you are on the green route (except part 2) is the last page of Bell's diary: on the green route one phrase is not erased.
At some point you'll have to recall details about Bell. If you make no mistakes, you get to the true ending (right route) and earn The First Wish of Bell achievement. If you make at least one mistake, you earn Drizzle achievement (left route).
Though every detail is mentioned, there's one tricky question. I will state short answers to the questions: red, old sweaters, bit, waist, Roller Coaster of Death, hand, thunders, dried.

You thought that was all? No, it wasn't. Reaching True Ending unlocks two more chapters in the Gallery (in the Title Screen). Both of them are linear.
Story of Another World
This is, as the name states, story where alternative timeline is created. By completing it you receive Gift achievement.
Nameless Dark Room
This is chapter where developer team shares their impressions about the game. The name itself is a reference to the Nameless Anime Club, members of which created the game. By hearing out what the developers have to say, you get the Tea Time at the Unnamed Club achievement.
Have you noticed one more achievement is missing and there's no more stories to read? But there's one story to watch! At the Nameless Dark Room Wutong hints there's a button at the title interface. It gets unlocked after achieving True Ending as well, so you can get it without reading additional chapters. Click on the cat and get Picture of Summer. And yes, video abrupts at some point, it's not a bug.