Learn to think in connections.

Why a second brain

Most note apps are filing cabinets. You write something down, drop it in a folder, and never see it again — because remembering to look is now your job. Your best ideas pile up in places you'll never reopen.

Cortex works differently. Instead of filing thoughts away, you connect them — and the app actively brings the right past note back to you at the moment it's useful. The goal isn't to store more. It's to think better: to notice patterns, build on yesterday's thinking, and turn a hundred small notes into something larger than their sum.

People call this a "second brain." You don't need to take that literally. Just hold onto one idea: a note becomes valuable the moment it connects to another.

The core loop

Everything in Cortex comes down to three repeating moves. Learn these and you've learned the whole tool.

1 · Capture   Get the thought down — fast, messy, now.
2 · Connect   Link it to ideas you already have.
3 · Resurface Cortex brings the right notes back as you think.

You don't do these in a strict order. You capture all day, connect when it's natural, and the resurfacing happens on its own. Over weeks, the loop compounds: each new note makes the others easier to find and more useful.

Your first ten minutes

Don't plan a system. Don't make folders. Just do this:

1. Open Today

The Today tab is a fresh note dated to today — your daily landing pad. Write whatever's on your mind: what you're working on, a question, something you read. This is the easiest habit to start and the one that makes everything else click.

2. Capture a loose thought

Tap the + (or the capture box) and jot a single idea — half a sentence is fine. It lands in your Inbox, a holding pen for thoughts you haven't placed yet. Capturing should feel like dropping a coin in a jar: no decisions, no friction.

3. Write one real note

Go to Notes and write a note about one thing you actually care about — a concept, a person, a project. Give it a clear title. That title matters: it's how you'll link to this note later.

Capturing well

The first rule of a second brain: capture beats organize. A thought you wrote down messily is worth infinitely more than the perfect one you lost. So lower the bar all the way.

• Capture before you judge. Don't decide if an idea is "good" yet — just get it in. You can refine later; you can't recover what you never wrote.
• One thought per capture. Resist cramming. Small, single thoughts are easier to connect later.
• Use the Inbox as a runway, not a graveyard. It's fine for things to sit there briefly. The point is to get them somewhere, then process them when you have a moment.
• Capture from anywhere. On your phone, share a link or a paragraph straight into Cortex — it arrives in your Inbox ready to connect.

The one skill that changes everything: linking

If you learn only one thing here, learn this. Links are what turn notes into thinking.

How to link

Anywhere you're writing, type two square brackets — [[ — and Cortex suggests your existing notes. Pick one (or type a new name) and you've created a link. It looks like this:

Usage-based pricing might reduce
churn — needs to fit our [[Revenue model]]
and we should weigh it against
[[Flat tiers]].   #strategy

Backlinks: the part that feels like magic

When you link from note A to note B, note B automatically gains a backlink — a record that says "A mentions me," with the sentence around it. Open any note and you can see everywhere it's referenced, without ever maintaining a list yourself. Over time this is how forgotten context finds its way back: you open "Revenue model" and discover five notes that quietly depend on it.

When to link

Link whenever you mention something that could be its own idea — a concept, a person, a project, a decision, a source. A good instinct: if you might ever write more about it, make it a link. An empty link (a note that doesn't exist yet) is fine — it's a promise to your future self, and Cortex will happily resolve it the moment you create that note.

Stop filing, start linking

Newcomers almost always make the same mistake: they try to design the perfect folder hierarchy before writing anything. Don't. Folders force every note into exactly one place — but ideas belong in many places at once. A note about "pricing" is also about "strategy," "the Q3 plan," and "that competitor."

So lean on links instead of folders. Let structure emerge from how your notes actually connect, rather than imposing it up front. A few light touches help:

• Map notes. When a topic grows, make a note that's just a list of links into it — a hand-made table of contents. Link to it from related notes and you have a hub you can always return to.
• Tags for states, links for meaning. Use a tag like #draft or #someday for a note's status; use [[links]] for what a note is about. Links connect ideas; tags filter them.
• Let the Graph show you the shape. The Graph tab draws your notes as a map. Dense clusters are your real areas of focus; lonely dots are ideas waiting to be connected.

Let the AI help you think

Cortex's AI isn't a chatbot you have to prompt. It works quietly in the background — and it runs entirely on your device, so nothing you write is uploaded. There are four ways it helps:

Search by meaning, not just words

Keyword search finds the exact words you type. ✦ Smart search finds notes by meaning — so searching "how should we make money?" can surface your "usage-based pricing" note even though it never used those words. Use Smart search when you remember the gist but not the phrasing.

Forgotten Knowledge

As you write, Cortex quietly resurfaces a related note you'd forgotten — at most one, never a barrage. This is the heart of thinking better: you're working on something new, and the app reminds you that you already had a relevant thought last month. Connect them, and your thinking compounds.

Insights

The Insights tab notices patterns across your whole vault: the themes you keep returning to, the notes that have become hubs, the orphans nothing links to yet, and pairs of notes that look related but aren't connected — with a nudge to link them.

Workflows & recipes

Cortex is just files and links, so it bends to whatever you do. Here are proven starting points — adopt one, not all.

Daily thinking journal

Start each day in Today. Brain-dump, then link the bits that connect to ongoing notes ([[Project X]], [[A person]]). Your daily notes become a time-stamped thread that ties everything else together.

Reading & research

For each source, make a note titled for it. In your own words, capture the claims and ideas — not long quotes. Link each claim to the concept it's about. Now your reading isn't a pile of highlights; it's connected to what you already think.

# Deci & Ryan, 1985
- intrinsic motivation beats reward
  → supports [[Motivation]]
- contradicts [[Carrot-and-stick]]
#source

Meetings

One note per meeting (the Meeting template gives you agenda / notes / action items). Link people and projects so the meeting connects into the rest of your knowledge instead of vanishing.

Projects

Give each project a "map" note that links to its tasks, decisions, and references. It becomes the place you start whenever you pick the project back up.

Decisions

When you decide something that matters, write a short note: the decision, why, and what you considered. Link it from the project. Six months later, "why did we choose this?" has an answer.

Developing an idea over time

This is where it all pays off. Capture a rough thought today. Add context next week. Link two related concepts next month. When Cortex resurfaces the right notes, a pattern appears — and the essay, plan, or decision half-writes itself, because the thinking was already there, connected.

Principles for thinking better

The tool is simple. The leverage comes from a few habits of mind:

• One idea per note (atomic notes). Small, single-idea notes connect in more ways and stay reusable. A sprawling note about ten things links to nothing well.
• Write in your own words. Rephrasing forces understanding. Copy-pasting feels productive but teaches you nothing and connects to nothing.
• Link as you write, not later. The best moment to make a connection is when you're already thinking about it.
• Make notes evergreen. Write so a note is still useful out of context — as if a stranger (future you) will read it cold.
• Favor connection over collection. Saving things is easy and addictive. The value is in linking and revisiting, not hoarding.
• Review to remember. Wander your notes. Re-reading and re-linking is where ideas mature.

Making it a habit

A second brain works only if it's a reflex. Keep it tiny and consistent:

• Daily: open Today, write a few lines, capture loose thoughts as they come.
• When you write: link anything you mention that could be its own note.
• Every few days: clear the Inbox — turn captures into real notes, or link and let them go.
• Weekly: a 10-minute review. Skim recent notes, follow a few links, check Insights, and connect anything obvious. This single habit is what makes the whole system compound.

Common beginner mistakes

• Designing a system before writing. You don't know your structure yet — it emerges. Just start capturing and linking.
• Hoarding without linking. A thousand orphan notes is a junk drawer. Even one link per note changes everything.
• Over-organizing with folders. Deep folder trees fight the way ideas overlap. Reach for links and tags first.
• Copy-pasting instead of rephrasing. If you didn't put it in your own words, you didn't really think it.
• Waiting for "perfect" notes. Notes are alive; they improve every time you return. Write the rough version now.
• Never revisiting. Capture without review is just a slower way to forget. The weekly skim is non-negotiable.

Your notes are yours

One thing to relax about: you can't get locked in. Every note is a plain Markdown file on your device (or a folder you choose). You can open them in any editor, back them up however you like, and leave any time by simply copying a folder. The AI runs on your device; nothing is uploaded and no account is required. Build with confidence — this knowledge is permanently yours.

Quick reference

The five surfaces

Essential moves