diff --git a/src/resources/extensions/gsd/bootstrap/register-hooks.ts b/src/resources/extensions/gsd/bootstrap/register-hooks.ts
index 438d4d9b0..ff6aefa83 100644
--- a/src/resources/extensions/gsd/bootstrap/register-hooks.ts
+++ b/src/resources/extensions/gsd/bootstrap/register-hooks.ts
@@ -181,14 +181,10 @@ export function registerHooks(pi: ExtensionAPI): void {
     // Only gate-shaped ask_user_questions calls should block execution.
     // The gate stays pending until the user selects the approval option.
     if (event.toolName === "ask_user_questions") {
-      const milestoneId = getDiscussionMilestoneId(discussionBasePath);
-      const inDiscussion = milestoneId !== null || isQueuePhaseActive();
-      if (inDiscussion) {
-        const questions: any[] = (event.input as any)?.questions ?? [];
-        const questionId = questions.find((question) => typeof question?.id === "string" && isGateQuestionId(question.id))?.id;
-        if (typeof questionId === "string") {
-          setPendingGate(questionId);
-        }
+      const questions: any[] = (event.input as any)?.questions ?? [];
+      const questionId = questions.find((question) => typeof question?.id === "string" && isGateQuestionId(question.id))?.id;
+      if (typeof questionId === "string") {
+        setPendingGate(questionId);
       }
     }
 
@@ -286,7 +282,6 @@ export function registerHooks(pi: ExtensionAPI): void {
     if (event.toolName !== "ask_user_questions") return;
     const milestoneId = getDiscussionMilestoneId(process.cwd());
     const queueActive = isQueuePhaseActive();
-    if (!milestoneId && !queueActive) return;
 
     const details = event.details as any;
 
@@ -319,13 +314,16 @@ export function registerHooks(pi: ExtensionAPI): void {
         // Only unlock the gate if the user selected the first option (confirmation).
         // Cross-references against the question's defined options to reject free-form "Other" text.
         const answer = details.response?.answers?.[question.id];
+        const inferredMilestoneId = extractDepthVerificationMilestoneId(question.id) ?? milestoneId;
         if (isDepthConfirmationAnswer(answer?.selected, question.options)) {
-          markDepthVerified(extractDepthVerificationMilestoneId(question.id) ?? milestoneId);
+          markDepthVerified(inferredMilestoneId);
+          clearPendingGate();
         }
         break;
       }
     }
 
+    if (!milestoneId && !queueActive) return;
     if (!milestoneId) return;
 
     const basePath = process.cwd();
diff --git a/src/resources/extensions/gsd/tests/register-hooks-depth-verification.test.ts b/src/resources/extensions/gsd/tests/register-hooks-depth-verification.test.ts
new file mode 100644
index 000000000..8e717234e
--- /dev/null
+++ b/src/resources/extensions/gsd/tests/register-hooks-depth-verification.test.ts
@@ -0,0 +1,97 @@
+import test from "node:test";
+import assert from "node:assert/strict";
+import { mkdirSync, rmSync } from "node:fs";
+import { join } from "node:path";
+import { tmpdir } from "node:os";
+
+import { registerHooks } from "../bootstrap/register-hooks.ts";
+import {
+  getPendingGate,
+  resetWriteGateState,
+  shouldBlockContextArtifactSave,
+} from "../bootstrap/write-gate.ts";
+
+function makeTempDir(prefix: string): string {
+  const dir = join(
+    tmpdir(),
+    `gsd-depth-gate-${prefix}-${Date.now()}-${Math.random().toString(36).slice(2, 8)}`,
+  );
+  mkdirSync(dir, { recursive: true });
+  return dir;
+}
+
+test("register-hooks unlocks milestone depth verification from question id without guided-flow state (#4047)", async (t) => {
+  const dir = makeTempDir("manual");
+  const originalCwd = process.cwd();
+  process.chdir(dir);
+  resetWriteGateState();
+
+  t.after(() => {
+    resetWriteGateState();
+    process.chdir(originalCwd);
+    rmSync(dir, { recursive: true, force: true });
+  });
+
+  const handlers = new Map<string, Array<(event: any, ctx?: any) => Promise<void> | void>>();
+  const pi = {
+    on(event: string, handler: (event: any, ctx?: any) => Promise<void> | void) {
+      const existing = handlers.get(event) ?? [];
+      existing.push(handler);
+      handlers.set(event, existing);
+    },
+  } as any;
+
+  registerHooks(pi);
+
+  const questionId = "depth_verification_M001_confirm";
+  const questions = [
+    {
+      id: questionId,
+      question: "Do you agree?",
+      options: [
+        { label: "Yes, you got it (Recommended)" },
+        { label: "Needs adjustment" },
+      ],
+    },
+  ];
+
+  const toolCallHandlers = handlers.get("tool_call");
+  const toolResultHandlers = handlers.get("tool_result");
+  assert.ok(toolCallHandlers?.length, "tool_call handler should be registered");
+  assert.ok(toolResultHandlers?.length, "tool_result handler should be registered");
+
+  for (const handler of toolCallHandlers ?? []) {
+    await handler({
+      toolName: "ask_user_questions",
+      input: { questions },
+    });
+  }
+
+  assert.equal(getPendingGate(), questionId, "gate should be set even without guided-flow state");
+  assert.equal(
+    shouldBlockContextArtifactSave("CONTEXT", "M001").block,
+    true,
+    "milestone context should still be blocked before confirmation",
+  );
+
+  for (const handler of toolResultHandlers ?? []) {
+    await handler({
+      toolName: "ask_user_questions",
+      input: { questions },
+      details: {
+        response: {
+          answers: {
+            [questionId]: { selected: "Yes, you got it (Recommended)" },
+          },
+        },
+      },
+    });
+  }
+
+  assert.equal(getPendingGate(), null, "confirming the depth question should clear the pending gate");
+  assert.equal(
+    shouldBlockContextArtifactSave("CONTEXT", "M001").block,
+    false,
+    "question-id milestone inference should unlock the matching milestone context write",
+  );
+});