You could also try Minder. It's not for handling plots, but you could use it for a graphic overview and organizing of your plots and stories, and then one of the tools suggested in the answers above just for text-handling part of it.
You can install Minder from the AppCenter (if you use a Linux-based OS). But there are also similar software for windows, and ...
You could try WikidPad. It is basically localised Wiki software with all the inter-linking features you may expect from such a tool. I've been using it to organise all my writing and outlining for nearly a year now, and I've yet to doubt it.
The only downside, if I could name one, is that 'pages' can't have one-word or purely numerical titles. I mainly ...
You might use Twine
This is an open source tool that is originally made to create interactive stories.
So, writing in blocks and visualize the structure of your story can be easily done.
If you use the "online" version (means only without installing), you can still use it offline (everything is inside your web browser).
But remember to backup (archive) ...
You could use either YWriter or Shaxpir to move parts of a manuscript around and rearrange things.
Not strictly for writing but you could use ToDoist as a simple outlining tool, or else try something like Trello, Asana or even Evernote to write a bunch of notes inside a project file and then mobe them around as needed.
I personally have 2 (free) accounts on Evernote, that share almost all notes, meaning I can use them on all my devices. There are online and downloaded versions of the notes application for all devices to my knowledge, and you can create notes or "notebooks" (notebooks contain multiple notes) for things such as "characters", "world", "plot points", ...
Professional editors for translators like memoq have this feature.
However, there is a good free solution as well, using vim if you are not scared of the command line.
Install a vim editor. Mac OS X has it pre-installed, for windows you need to download it for free.
Learn some vim basics (how to open a file, save, quit the editor etc), it's boring but you ...