http://twinery.org/2/
In the main screen, you see all your stories. If you use this software on this website, and not as standalone application, make sure to archive your stories once in a while (button on the right side).
Click on +Story to start a new one. Name it and you will see the story graph. A story consists of many connected passages. In the beginning, there is only one. The green rocket indicates that this is where the story starts.
Twine has several story formats, the default one is called "Harlowe". There are others, and you can switch between them by clicking on your story name in the bottom left and selecting "Change story format". I'm using SugarCube2, because it's the most advanced one.
Now double click the first passage to edit it.
In the edit window, you can write normal text. Now write something like this:
Code: Select all
[[Choice A]]
[[Choice B]]
Click on the play button in the bottom right. After your story text, you should see two links that move the reader to the next passage.
To make your story more interactive, read up on your selected story format (e.g. SugarCube: http://www.motoslave.net/sugarcube/2/). You can easily set and display values, create an inventory, optional or timed passages, and even use Javascript if you are so inclined.
You can find more extensive documentation here:
http://twinery.org/wiki/twine2:guide