diff --git a/src/resources/extensions/gsd/auto-start.ts b/src/resources/extensions/gsd/auto-start.ts
index 8751d51c7..a3d0232d5 100644
--- a/src/resources/extensions/gsd/auto-start.ts
+++ b/src/resources/extensions/gsd/auto-start.ts
@@ -44,6 +44,9 @@ import {
   nativeInit,
   nativeAddAll,
   nativeCommit,
+  nativeGetCurrentBranch,
+  nativeDetectMainBranch,
+  nativeCheckoutBranch,
 } from "./native-git-bridge.js";
 import { GitServiceImpl } from "./git-service.js";
 import {
@@ -528,6 +531,22 @@ export async function bootstrapAutoSession(
       setActiveMilestoneId(base, s.currentMilestoneId);
     }
 
+    // Guard against stale milestone branch when isolation:none (#3613).
+    // A prior session with isolation:branch/worktree may have left HEAD on
+    // milestone/<MID>. Auto-checkout back to the integration branch.
+    if (getIsolationMode() === "none" && nativeIsRepo(base)) {
+      try {
+        const currentBranch = nativeGetCurrentBranch(base);
+        if (currentBranch.startsWith("milestone/")) {
+          const integrationBranch = nativeDetectMainBranch(base);
+          nativeCheckoutBranch(base, integrationBranch);
+          logWarning("bootstrap", `Returned to "${integrationBranch}" — HEAD was on stale milestone branch "${currentBranch}" (isolation: none does not use milestone branches).`);
+        }
+      } catch (err) {
+        logWarning("bootstrap", `Could not auto-checkout from stale milestone branch: ${err instanceof Error ? err.message : String(err)}`);
+      }
+    }
+
     // ── Auto-worktree setup ──
     s.originalBasePath = base;
 
diff --git a/src/resources/extensions/gsd/tests/isolation-none-branch-guard.test.ts b/src/resources/extensions/gsd/tests/isolation-none-branch-guard.test.ts
new file mode 100644
index 000000000..5acf71583
--- /dev/null
+++ b/src/resources/extensions/gsd/tests/isolation-none-branch-guard.test.ts
@@ -0,0 +1,62 @@
+/**
+ * Regression test for #3675 — isolation:none stale branch guard
+ *
+ * When switching from isolation:branch/worktree to isolation:none, HEAD
+ * could remain on a milestone/<MID> branch. The fix in auto-start.ts
+ * detects this and auto-checks out to the integration branch.
+ *
+ * This structural test verifies the milestone/ branch check exists
+ * in auto-start.ts.
+ */
+
+import { describe, test } from 'node:test';
+import assert from 'node:assert/strict';
+import { readFileSync } from 'node:fs';
+import { fileURLToPath } from 'node:url';
+import { dirname, join } from 'node:path';
+
+const __filename = fileURLToPath(import.meta.url);
+const __dirname = dirname(__filename);
+
+const source = readFileSync(join(__dirname, '..', 'auto-start.ts'), 'utf-8');
+
+describe('isolation:none stale branch guard (#3675)', () => {
+  test('checks for milestone/ branch prefix', () => {
+    assert.match(source, /startsWith\(["']milestone\//,
+      'auto-start should check for milestone/ branch prefix');
+  });
+
+  test('imports nativeGetCurrentBranch', () => {
+    assert.match(source, /nativeGetCurrentBranch/,
+      'auto-start should import nativeGetCurrentBranch');
+  });
+
+  test('imports nativeDetectMainBranch', () => {
+    assert.match(source, /nativeDetectMainBranch/,
+      'auto-start should import nativeDetectMainBranch');
+  });
+
+  test('imports nativeCheckoutBranch', () => {
+    assert.match(source, /nativeCheckoutBranch/,
+      'auto-start should import nativeCheckoutBranch');
+  });
+
+  test('guard is conditional on isolation mode "none"', () => {
+    assert.match(source, /getIsolationMode\(\)\s*===\s*["']none["']/,
+      'guard should only activate when isolation mode is "none"');
+  });
+
+  test('calls nativeCheckoutBranch to return to integration branch', () => {
+    assert.match(source, /nativeCheckoutBranch\(base,\s*integrationBranch\)/,
+      'should checkout to the integration branch');
+  });
+
+  test('guard is wrapped in try-catch (non-fatal)', () => {
+    // Find the milestone/ check and verify it is inside a try block
+    const milestoneIdx = source.indexOf('startsWith("milestone/")');
+    assert.ok(milestoneIdx > 0, 'milestone/ check should exist');
+    const before = source.slice(Math.max(0, milestoneIdx - 500), milestoneIdx);
+    assert.match(before, /try\s*\{/,
+      'milestone branch guard should be inside a try block');
+  });
+});