diff --git a/src/commands/sync.ts b/src/commands/sync.ts
index 0e857003b..4737501e8 100644
--- a/src/commands/sync.ts
+++ b/src/commands/sync.ts
@@ -1628,7 +1628,44 @@ async function performSyncInner(engine: BrainEngine, opts: SyncOpts): Promise<Sy
   //   - syncScopeRoot:  file walking, imports, deletes, renames
   // In the common case (repoPath == git root, no subpath) they are identical.
   serr(`[gbrain phase] sync.discover_git_root`);
-  const gitContextRoot = realpathSync(discoverGitRoot(repoPath));
+  // #2964: a legacy `sync.repo_path`-anchored default brain (no `sources`
+  // row, no `opts.sourceId`) can reach here having never been `git init`-ed
+  // — e.g. a brain-pages dir that predates git-backed sync, or one rsync'd
+  // from another machine without its `.git`. gbrain owns this directory
+  // outright (it's not a user-external path the way an `opts.sourceId` +
+  // local `sources add --path` entry is), so self-heal by initializing it
+  // in place instead of failing the sync phase every single run. Mirrors
+  // the recloneIfMissing self-recovery above for owned remote clones.
+  // Scoped to !opts.sourceId only — a registered local source without a
+  // remote_url stays a loud, actionable error (it's the user's own
+  // directory; silently git-initializing it without consent is an
+  // overreach).
+  let gitContextRoot: string;
+  try {
+    gitContextRoot = realpathSync(discoverGitRoot(repoPath));
+  } catch (err) {
+    if (opts.sourceId || !existsSync(repoPath)) throw err;
+    serr(`[gbrain] auto-recovery: git-initializing brain dir ${repoPath} (no git repo found).`);
+    git(repoPath, ['init', '--quiet']);
+    // A fresh `git init` has zero commits, and `git rev-parse HEAD` a few
+    // lines below requires at least one — without a baseline commit we'd
+    // just trade "not a git repo" for "no commits in repo" on the very next
+    // line. Snapshot the CURRENT on-disk state as that baseline (respecting
+    // .gitignore, written first) so future incremental syncs diff against
+    // what's actually here rather than an empty tree — an empty initial
+    // commit would make every existing file look "added" again on the next
+    // sync, even though this full-sync pass already imported them.
+    manageGitignore(repoPath, engine.kind);
+    git(repoPath, ['add', '-A']);
+    // Explicit identity via -c: a headless nightly cron/launchd invocation
+    // has no reason to have global git user.name/user.email configured.
+    git(
+      repoPath,
+      ['commit', '--quiet', '--allow-empty', '-m', 'gbrain: initial commit (auto-init by sync)'],
+      ['user.name=gbrain', 'user.email=gbrain@localhost'],
+    );
+    gitContextRoot = realpathSync(discoverGitRoot(repoPath));
+  }
   const rawScopeRoot = opts.srcSubpath ? join(repoPath, opts.srcSubpath) : repoPath;
   if (!existsSync(rawScopeRoot)) {
     throw new Error(`Sync scope does not exist: ${rawScopeRoot}`);
diff --git a/test/sync-git-autoinit.test.ts b/test/sync-git-autoinit.test.ts
new file mode 100644
index 000000000..6a55af938
--- /dev/null
+++ b/test/sync-git-autoinit.test.ts
@@ -0,0 +1,112 @@
+/**
+ * #2964 — sync phase self-heals a never-git-initialized default brain dir.
+ *
+ * A legacy `sync.repo_path`-anchored default brain (no `sources` row, no
+ * `--source`) can reach `performSync` pointed at a directory that was never
+ * `git init`-ed (predates git-backed sync, or was rsync'd from another
+ * machine without its `.git`). Before this fix, `discoverGitRoot` threw
+ * unconditionally and the dream cycle's sync phase failed every night with
+ * no self-recovery, even though `doctor`'s sync checks reported "ok" (for
+ * an unrelated reason — they only look at the `sources` table, which has
+ * no rows for this kind of brain).
+ *
+ * gbrain owns this directory outright, so the fix self-heals by
+ * `git init`-ing it and capturing the current on-disk state as the sync
+ * baseline — but ONLY for the default/no-`sourceId` path. A registered
+ * local source (`sources add --path`, no `--url`) is the user's own
+ * external directory and must keep failing loudly rather than being
+ * silently git-initialized without consent.
+ */
+
+import { describe, test, expect, beforeAll, afterAll, beforeEach, afterEach } from 'bun:test';
+import { mkdtempSync, writeFileSync, rmSync, existsSync } from 'fs';
+import { join } from 'path';
+import { tmpdir } from 'os';
+import { PGLiteEngine } from '../src/core/pglite-engine.ts';
+import { resetPgliteState } from './helpers/reset-pglite.ts';
+
+function mdPage(title: string, body = 'Content.'): string {
+  return `---\ntype: note\ntitle: ${title}\n---\n\n${body}`;
+}
+
+describe('#2964: sync auto-inits a never-git-initialized default brain dir', () => {
+  let engine: PGLiteEngine;
+  let dir: string;
+
+  beforeAll(async () => {
+    engine = new PGLiteEngine();
+    await engine.connect({});
+    await engine.initSchema();
+  }, 60_000);
+
+  afterAll(async () => {
+    await engine.disconnect();
+  }, 60_000);
+
+  beforeEach(async () => {
+    await resetPgliteState(engine);
+    dir = mkdtempSync(join(tmpdir(), 'gbrain-2964-'));
+    writeFileSync(join(dir, 'page1.md'), mdPage('Page 1'));
+    writeFileSync(join(dir, 'page2.md'), mdPage('Page 2'));
+  });
+
+  afterEach(() => {
+    if (dir) rmSync(dir, { recursive: true, force: true });
+  });
+
+  test('default (no sourceId) sync on a non-git dir auto-inits git and imports files', async () => {
+    const { performSync } = await import('../src/commands/sync.ts');
+    expect(existsSync(join(dir, '.git'))).toBe(false);
+
+    const result = await performSync(engine, {
+      repoPath: dir,
+      noPull: true,
+      noEmbed: true,
+      full: true,
+    });
+
+    expect(result.status).toBe('first_sync');
+    expect(result.added).toBe(2);
+    expect(existsSync(join(dir, '.git'))).toBe(true);
+    expect(await engine.getPage('page1')).not.toBeNull();
+    expect(await engine.getPage('page2')).not.toBeNull();
+  });
+
+  test('a second sync after auto-init sees no changes (baseline commit captured current on-disk state)', async () => {
+    const { performSync } = await import('../src/commands/sync.ts');
+    const first = await performSync(engine, {
+      repoPath: dir,
+      noPull: true,
+      noEmbed: true,
+      full: true,
+    });
+    expect(first.added).toBe(2);
+
+    // No new files, no explicit `full` — a real incremental sync against the
+    // auto-init baseline. Before this fix there was no baseline to diff
+    // against (sync errored outright); a naive fix that skipped the initial
+    // commit would make this call re-report both files as "added" again.
+    const second = await performSync(engine, {
+      repoPath: dir,
+      noPull: true,
+      noEmbed: true,
+    });
+    expect(second.status).not.toBe('first_sync');
+    expect(second.added).toBe(0);
+    expect(second.modified).toBe(0);
+  });
+
+  test('a registered local source (sourceId set, no remote_url) on a non-git dir still throws — not auto-inited', async () => {
+    const { performSync } = await import('../src/commands/sync.ts');
+    await expect(
+      performSync(engine, {
+        repoPath: dir,
+        sourceId: 'default',
+        noPull: true,
+        noEmbed: true,
+        full: true,
+      }),
+    ).rejects.toThrow(/git repository/i);
+    expect(existsSync(join(dir, '.git'))).toBe(false);
+  });
+});