The Annotator plugin allows users to open and annotate PDF and EPUB files within Obsidian. It enables storing annotations locally in markdown files, maintaining a structured workflow without relying on external services. Users can highlight text, add comments, and link annotations directly to their notes for better organization. The plugin supports dark mode, provides an option to toggle between annotation and markdown modes, and integrates with the Dataview plugin for enhanced querying capabilities. Annotations are easily accessible via Obsidian links, ensuring smooth navigation between notes and files.