How to Build an AI Second Brain Using Claude Fable 5 & Obsidian

I had over 2,000 notes saved across Notion, Apple Notes, and random Google Docs. I hadn't opened most of them in months.

All that research I did on AI tools last year. Meeting notes from client calls. Ideas I had at midnight that felt important at the time. All of it sitting in folders I never touched, completely useless.

Then I started connecting Claude directly to Obsidian and the whole thing changed.

And with the release of Claude Fable 5, this setup just got a serious upgrade.

Here's exactly how to build it, even if you've never used either tool before.

What Is Claude Fable 5 and Why It Matters Here

Claude Fable 5 is the first model in Anthropic's new Claude 5 family, and it's part of a brand new model tier called Mythos-class — a tier that sits above Claude Opus in capability. It's the most intelligent Claude model that's generally available right now.

Why does that matter for a second brain?

Because the whole point of this system is reasoning across hundreds of interconnected notes. Finding the connection between a research note from January and a client call from last week. Spotting patterns across months of thinking. Following chains of wikilinks five notes deep and coming back with an insight you never would have found yourself.

That's exactly the kind of deep, multi-step reasoning where a more capable model shows up the most. Summarizing one note? Any model can do that. Synthesizing your entire vault into something useful? That's where Fable 5 earns its place at the top of the lineup.

You can use Fable 5 everywhere this guide touches: in the claude.ai app, in Claude Code, and through the API (model string: claude-fable-5). One model, every workflow below.

For the full breakdown of the Claude 5 family, Anthropic's announcement is at anthropic.com/news/claude-fable-5-mythos-5.

Now let's build the system.

Why Obsidian and Not Notion, Apple Notes, or Google Docs

The answer is simpler than most people think.

Obsidian stores your notes as plain markdown files on your computer. That's it. No proprietary format. No cloud lock-in. No subscription for the core features. Just folders of .md files sitting on your hard drive.

Any AI can read a markdown file. You point Claude Fable 5 at your vault and it reads every note without exporting, converting, or uploading anything. You can switch AI providers anytime without migrating your notes. You can version control your whole vault with Git.

Notion locks your notes in a database. Apple Notes locks them in iCloud. Google Docs locks them in Google's format. Every one of those creates friction when you try to connect AI to them.

Obsidian has none of that friction. Your notes are just files. AI reads files.

The other big advantage is bidirectional links. When you write [[project name]] in a note, it automatically connects to every other note that mentions that project. Over time you build a web of connected knowledge instead of a flat list of isolated documents.

Fable 5 can follow those links. It finds connections between your notes that you never made yourself. Patterns across hundreds of notes you'd never find manually — and this is exactly where the extra reasoning power of a Mythos-class model pays off.

That's the real advantage here. Not just AI plus notes. The smartest available AI plus connected notes.

Step 1: Set Up Your Vault

Download Obsidian from obsidian.md. It's free. Install it. Create a new vault — this is just a folder on your computer where all your notes live.

Create this folder structure inside it:

Inbox/ — where new notes land before they're organized. Every idea and quick capture goes here first.

Projects/ — active projects. One folder per project.

Areas/ — ongoing areas of responsibility. Things like "Marketing," "Finance," "Health" — whatever categories matter to your life or work.

Resources/ — reference material. Research, articles, book notes, course notes, templates.

Archive/ — completed projects and outdated stuff. Still searchable but out of your active view.

This comes from Tiago Forte's PARA method and it works really well with AI because it gives Fable 5 clear categories to reason about.

Don't overthink this part. The structure can change. The worst thing you can do is spend three days designing the perfect folder system instead of actually putting notes in it.

Step 2: Start Taking Notes the Right Way

Here's where most Obsidian guides go wrong. They teach you the tool before teaching you the habit.

The habit is simple: capture anything that might be useful later.

When you read something with a useful insight, open Obsidian and write a quick note about it. Not a copy-paste of the article. A few sentences in your own words about why it matters to you.

When you have an idea, put it in the Inbox folder.

When you finish a meeting, spend two minutes writing the key decisions and next steps.

The formatting doesn't matter at first. The consistency does.

Here's what makes a note AI-friendly:

Use a clear title. "Meeting Notes 2026-05-30 — Product Roadmap Review" not just "notes."

Use frontmatter. At the top of every note:

---

tags: [meeting-notes, product, q2-2026]

date: 2026-05-30

project: "[[Product Roadmap]]"

---

Use wikilinks. When you mention a person, project, or concept that has its own note, link to it: [[Ray Fu]], [[Q2 Launch Plan]], [[Customer Retention Strategy]]. These are what build the connected web that makes the whole system work.

Write for your future self. Assume you'll forget all context in three months. Include enough detail that the note makes sense on its own.

Step 3: Connect Claude Fable 5 to Your Vault

There are three ways to do this depending on your comfort level. In every option, make sure Fable 5 is the model you've selected — it's the one you want reasoning over your knowledge base.

Option A: Claude.ai Projects (Easiest — No Technical Setup)

Create a Project in claude.ai. Upload your most important notes as project knowledge files. Every conversation in that project now has access to those notes, with Fable 5 doing the thinking.

Limitations: you have to manually upload files, there's a size limit, and it doesn't auto-sync when you update your notes.

Best for testing the concept before committing to a deeper setup.

Option B: Claude Code + Direct Vault Access (Most Powerful)

Point Claude Code directly at your Obsidian vault folder. Claude can read, search, and write to your vault files — and with Fable 5 under the hood, it can handle the kind of vault-wide reasoning tasks that used to require breaking everything into smaller chunks.

In your CLAUDE.md file, add:

> "My Obsidian vault is located at ~/Documents/MyVault. Use it as a persistent knowledge base. When I ask questions, search relevant notes first. When you generate research or summaries, save them as new notes in the appropriate folder following the existing naming and formatting conventions."

This is what developers and power users are running right now. It's way more capable than any other approach.

Option C: MCP Servers (Best Balance of Power and Ease)

A few MCP servers are built specifically for Obsidian:

mcpvault — no dependencies, no plugin required, works without Obsidian running. Reads raw .md files directly with BM25 search and relevance ranking. 14 MCP methods. The cleanest option for most people.

mcp-obsidian — 3,000+ GitHub stars, more established. Requires the Local REST API community plugin, which means Obsidian must be running. More features but more setup.

Obsidian-Skills by Steph Ango — the CEO of Obsidian published official Claude Skills for Obsidian. 12,900+ GitHub stars. Five skills covering every Obsidian file format. These follow the open Agent Skills spec so they work with Claude Code and other agents.

Pick one. Install it. Now Fable 5 can reason over your entire knowledge base.

Step 4: Build Your First AI Workflows

Once Fable 5 can access your vault, start with these five.

Workflow 1: The Weekly Digest

> "Read all my notes tagged with #meeting-notes from the past week. Create a weekly summary that includes key decisions made, action items, open questions, and any patterns you notice across multiple meetings. Save it as a new note in Weekly Reviews/."

Fable 5 reads your meeting notes, finds the patterns, and delivers a summary you'd never have time to build yourself.

Workflow 2: The Research Synthesizer

> "I just saved three new research notes about [topic] in my Resources folder. Read them alongside any existing notes I have on this topic. Create a synthesis note that identifies the most important insights across all sources, flags contradictions, highlights knowledge gaps, and suggests what I should research next."

This is the workflow where the model upgrade is most obvious. Fable 5 doesn't just summarize each note separately — it finds the connections and contradictions between them, even across a large set of sources.

Workflow 3: The Idea Connector

> "Search my entire vault for notes related to [[Current Project]] that aren't currently linked to it. Look for relevant insights, past research, and ideas I might have forgotten. List the top 10 connections with a one-sentence explanation of why each is relevant."

This surfaces buried knowledge. That idea you had six months ago that's suddenly relevant to what you're building right now? Fable 5 finds it.

Workflow 4: The Knowledge Gap Finder

> "Analyze my notes about [topic]. What subtopics haven't I written about? What questions have I explored but not answered? What areas does my vault cover shallowly? Create a list of knowledge gaps ranked by importance."

Instead of figuring out what you don't know on your own, let Fable 5 audit your knowledge base and tell you.

Workflow 5: The Daily Briefing

> "Read my daily notes from the past three days and my current project notes. Create a morning briefing with what I was working on, what I planned to do next, any deadlines in the next week, and suggestions for what to focus on today based on urgency and importance."

You wake up. Fable 5 already wrote you a briefing based on your own notes. You know exactly where you left off.

Step 5: Design Notes for AI From the Start

There's a concept called AI-first note design. Structure your notes so that AI can understand them as easily as you can.

In practice it looks like this:

Every note gets machine-readable frontmatter. Tags, dates, project links, status. This lets Fable 5 filter your vault efficiently.

Every note starts with one sentence that describes what it contains. "This note covers the key findings from our Q2 customer retention analysis." The model reads this first and decides whether the note is relevant before going through the full content.

Every note uses consistent formatting. Headers for sections. Bold for key terms. Links for relationships. When every note follows the same structure, Fable 5 can parse them reliably.

Sources get captured fully. URL, author, date, and a direct quote. This lets Fable 5 trace claims back to original sources when pulling from your vault.

It takes a little more time when creating notes. But it makes every future AI interaction way more useful.

Step 6: Let Fable 5 Maintain Your Vault

The reason most knowledge systems fail is maintenance. People are good at adding notes. Nobody is good at organizing, linking, and updating them consistently.

Fable 5 can do all of that.

> "Scan my Inbox folder for any notes that have been there for more than 3 days. For each one, suggest which folder it belongs in, add appropriate tags, and identify any existing notes it should be linked to."

> "Check all notes in Projects/ for any that reference completed projects. Move them to Archive/ and update any links that point to them."

> "Find notes in my vault with zero incoming links — no other notes link to them. For each one, identify 2-3 existing notes that should link to it and explain why."

You built the vault. Fable 5 keeps it organized. The system stays clean without you spending hours on it.

Step 7: The Compounding Effect

A second brain you use for one week is a note-taking app.

A second brain you use for one month is a useful reference system.

A second brain you use for six months is a knowledge engine that contains insights, connections, and accumulated understanding that no amount of Googling can replicate.

And when the most capable generally available model can access all of it, every new note you add becomes more valuable — because it doesn't sit in isolation. It connects to everything you've already written.

The person who builds this now and keeps it going for six months will have something genuinely hard to replicate. Their AI assistant will know their work, their research, their projects, and their thinking in a way that nobody else's AI can.

That's what a real second brain looks like. Not a folder full of files you forgot about. A system that actually thinks alongside you.

Start today. Download Obsidian. Create five notes about what you're working on right now. Connect Claude Fable 5. Ask it a question using your own notes.

That first moment when the smartest Claude model ever released answers using your own knowledge changes everything.

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