I just made a major shift in how I write my stories. For a while now, I have been using Obsidian for note taking. It stores notes as files in a folder structure using a markup language called Markdown (the editor on this site uses a simplified form of it, in fact). And somewhere along the line, I realized that I could actually just write my drafts in the Markdown editor in Obsidian so that my drafts and notes were all in the same place. If I need to do more sophisticated formatting, I can still switch over to LibreOffice Writer, and the latest release of LibreOffice actually supports importing Markdown files. Even better, the "vault" (as Obsidian calls it's folder) is just a folder on my hard drive with sub-folders beneath, so that I can copy files into and out of it just using Linux Mint's File Manager (or Windows Explorer if I'm on a Windows box). The maker of Obsidian offers relatively cheap synchronization using their own private cloud, too, so I can easily have access to my vault on multiple devices including my phone.
Right now, I have a folder in my vault for notes, with sub-folders for each idea or story, then another where I actually keep drafts. However, for a rather long, involved work I have been playing with (possibly a first novel), I created a folder in the vault just for it, with one subfolder for drafts and another for notes and planning (things like a timeline of the backstory and the various themes and questions I want to address). Makes for much better organization than having drafts and notes in different programs and also allows me to link between notes or between drafts and notes.
Main downside? No formatting beyond what Markdown supports. But for a draft that will go on here, that doesn't really matter. The text gets pasted into the StoriesSpace editor anyhow. For day to day writing, I don't really need much formatting. And, as I said, I can always import the Markdown files into LibreOffice for formatting.
So how are you writing these days? Word processor? A writing tool like Scrivener? Long hand (hey, Clive Barker and Neil Gaiman were still doing first drafts longhand last I heard)?