Step 3: Write your document
Turn your plan into a finished manuscript
No tool recommendation for this step — this is just the writing itself. Keep your Step 1 mindmap and Step 2 plot flowchart open in another tab as a reference, and don't worry about following them exactly; plans change once you're actually inside the story, and that's normal.
If you're tracking characters, relationships, or subplots in Amanuensis (Step 2), keep it updated as you write rather than all at once at the end — it's much easier to log a change when it happens than to reconstruct it from a finished draft.
Once you have a complete draft, move on to Step 4: Get it edited.