Still, nothing beats pen and papers for the beginning.
I totally agree. My slight variation -- but the same principle -- is a big whiteboard and post-it notes. This especially benefits branching content such as conversation trees and quest trees. Draw big boxes on the whiteboard for major topics and smaller boxes inside them for subtopics. Put post-its in the smaller boxes for details such as individual lines of dialogue, quest entries, etc. This way you can rearrange ideas and link content in different ways without having to fight software.
This also helps you transfer content more efficiently into branching content software like articy:draft, Chat Mapper, and Twine. The choice of software will often be dictated by the engineering side to accommodate their ability to bring your content into the game.
For an initial treatment, which is usually linear and doesn't get into the details of breaking down branches, good old pen and paper.
Whatever tools you use, make sure it has some way to do search and replace (e.g., changing an NPC's name halfway through the project), spell check, and localization, even if it's by means of exporting to formats that can do those things and then importing back into your tool.