diff --git a/src/resources/extensions/gsd/doctor.ts b/src/resources/extensions/gsd/doctor.ts
index 7c48f1075..44a3846bb 100644
--- a/src/resources/extensions/gsd/doctor.ts
+++ b/src/resources/extensions/gsd/doctor.ts
@@ -265,6 +265,21 @@ async function markTaskDoneInPlan(basePath: string, milestoneId: string, sliceId
   }
 }
 
+async function markTaskUndoneInPlan(basePath: string, milestoneId: string, sliceId: string, taskId: string, fixesApplied: string[]): Promise<void> {
+  const planPath = resolveSliceFile(basePath, milestoneId, sliceId, "PLAN");
+  if (!planPath) return;
+  const content = await loadFile(planPath);
+  if (!content) return;
+  const updated = content.replace(
+    new RegExp(`^(\\s*-\\s+)\\[x\\]\\s+\\*\\*${taskId}:`, "mi"),
+    `$1[ ] **${taskId}:`,
+  );
+  if (updated !== content) {
+    await saveFile(planPath, updated);
+    fixesApplied.push(`unchecked ${taskId} in ${planPath} (missing summary — task will re-execute)`);
+  }
+}
+
 async function markSliceDoneInRoadmap(basePath: string, milestoneId: string, sliceId: string, fixesApplied: string[]): Promise<void> {
   const roadmapPath = resolveMilestoneFile(basePath, milestoneId, "ROADMAP");
   if (!roadmapPath) return;
@@ -769,30 +784,13 @@ export async function runGSDDoctor(basePath: string, options?: { fix?: boolean;
             code: "task_done_missing_summary",
             scope: "task",
             unitId: taskUnitId,
-            message: `Task ${task.id} is marked done but summary is missing`,
-            file: relTaskFile(basePath, milestoneId, slice.id, task.id, "SUMMARY"),
+            message: `Task ${task.id} is marked done but summary is missing — unchecking so it re-executes`,
+            file: relSliceFile(basePath, milestoneId, slice.id, "PLAN"),
             fixable: true,
           });
-          dryRunCanFix("task_done_missing_summary", `create stub summary for ${taskUnitId}`);
+          dryRunCanFix("task_done_missing_summary", `uncheck ${task.id} in plan for ${taskUnitId}`);
           if (shouldFix("task_done_missing_summary")) {
-            const stubPath = join(
-              basePath, ".gsd", "milestones", milestoneId, "slices", slice.id, "tasks",
-              `${task.id}-SUMMARY.md`,
-            );
-            const stubContent = [
-              `---`,
-              `status: done`,
-              `result: unknown`,
-              `doctor_generated: true`,
-              `---`,
-              ``,
-              `# ${task.id}: ${task.title || "Unknown"}`,
-              ``,
-              `Summary stub generated by \`/gsd doctor\` \u2014 task was marked done but no summary existed.`,
-              ``,
-            ].join("\n");
-            await saveFile(stubPath, stubContent);
-            fixesApplied.push(`created stub summary for ${taskUnitId}`);
+            await markTaskUndoneInPlan(basePath, milestoneId, slice.id, task.id, fixesApplied);
           }
         }
 
diff --git a/src/resources/extensions/gsd/roadmap-mutations.ts b/src/resources/extensions/gsd/roadmap-mutations.ts
index 85119c5b3..a2a55b45c 100644
--- a/src/resources/extensions/gsd/roadmap-mutations.ts
+++ b/src/resources/extensions/gsd/roadmap-mutations.ts
@@ -93,3 +93,29 @@ export function markTaskDoneInPlan(basePath: string, planPath: string, tid: stri
   clearParseCache();
   return true;
 }
+
+/**
+ * Mark a task as not done ([ ]) in the slice plan.
+ * Idempotent — no-op if already unchecked or if the task isn't found.
+ *
+ * @returns true if the plan was modified, false if no change was needed
+ */
+export function markTaskUndoneInPlan(basePath: string, planPath: string, tid: string): boolean {
+  let content: string;
+  try {
+    content = readFileSync(planPath, "utf-8");
+  } catch {
+    return false;
+  }
+
+  const updated = content.replace(
+    new RegExp(`^(\\s*-\\s+)\\[x\\]\\s+\\*\\*${tid}:`, "mi"),
+    `$1[ ] **${tid}:`,
+  );
+
+  if (updated === content) return false;
+
+  atomicWriteSync(planPath, updated);
+  clearParseCache();
+  return true;
+}
diff --git a/src/resources/extensions/gsd/tests/atomic-task-closeout.test.ts b/src/resources/extensions/gsd/tests/atomic-task-closeout.test.ts
new file mode 100644
index 000000000..fab33427e
--- /dev/null
+++ b/src/resources/extensions/gsd/tests/atomic-task-closeout.test.ts
@@ -0,0 +1,184 @@
+/**
+ * Tests for atomic task closeout (#1650):
+ * 1. Doctor unmarks task checkbox when summary is missing (instead of creating stub)
+ * 2. markTaskUndoneInPlan correctly unchecks a task in the slice plan
+ */
+
+import { mkdirSync, writeFileSync, readFileSync, rmSync, existsSync } from "node:fs";
+import { join } from "node:path";
+import { tmpdir } from "node:os";
+import test from "node:test";
+import assert from "node:assert/strict";
+import { runGSDDoctor } from "../doctor.ts";
+import { markTaskUndoneInPlan } from "../roadmap-mutations.ts";
+
+function makeTmp(name: string): string {
+  const dir = join(tmpdir(), `atomic-closeout-${name}-${Date.now()}-${Math.random().toString(36).slice(2)}`);
+  mkdirSync(dir, { recursive: true });
+  return dir;
+}
+
+// ── markTaskUndoneInPlan ─────────────────────────────────────────────────────
+
+test("markTaskUndoneInPlan unchecks a checked task", () => {
+  const base = makeTmp("uncheck");
+  const planPath = join(base, "PLAN.md");
+  writeFileSync(planPath, `# S01: Demo
+
+## Tasks
+
+- [x] **T01: First task** \`est:5m\`
+- [ ] **T02: Second task** \`est:10m\`
+`);
+
+  const changed = markTaskUndoneInPlan(base, planPath, "T01");
+  assert.ok(changed, "should return true when plan was modified");
+
+  const content = readFileSync(planPath, "utf-8");
+  assert.ok(content.includes("- [ ] **T01:"), "T01 should be unchecked");
+  assert.ok(content.includes("- [ ] **T02:"), "T02 should remain unchecked");
+
+  rmSync(base, { recursive: true, force: true });
+});
+
+test("markTaskUndoneInPlan is idempotent on already-unchecked task", () => {
+  const base = makeTmp("uncheck-noop");
+  const planPath = join(base, "PLAN.md");
+  writeFileSync(planPath, `# S01: Demo
+
+## Tasks
+
+- [ ] **T01: First task** \`est:5m\`
+`);
+
+  const changed = markTaskUndoneInPlan(base, planPath, "T01");
+  assert.ok(!changed, "should return false when no change needed");
+
+  rmSync(base, { recursive: true, force: true });
+});
+
+test("markTaskUndoneInPlan handles indented checkboxes", () => {
+  const base = makeTmp("uncheck-indent");
+  const planPath = join(base, "PLAN.md");
+  writeFileSync(planPath, `# S01: Demo
+
+## Tasks
+
+  - [x] **T01: First task** \`est:5m\`
+`);
+
+  const changed = markTaskUndoneInPlan(base, planPath, "T01");
+  assert.ok(changed, "should handle indented checkboxes");
+
+  const content = readFileSync(planPath, "utf-8");
+  assert.ok(content.includes("[ ] **T01:"), "T01 should be unchecked");
+
+  rmSync(base, { recursive: true, force: true });
+});
+
+// ── Doctor: task_done_missing_summary unchecks instead of stubbing ────────────
+
+test("doctor unchecks task when checkbox is marked but summary is missing", async () => {
+  const base = makeTmp("doctor-uncheck");
+  const gsd = join(base, ".gsd");
+  const m = join(gsd, "milestones", "M001");
+  const s = join(m, "slices", "S01");
+  const t = join(s, "tasks");
+  mkdirSync(t, { recursive: true });
+
+  writeFileSync(join(m, "M001-ROADMAP.md"), `# M001: Test
+
+## Slices
+
+- [ ] **S01: Test Slice** \`risk:low\` \`depends:[]\`
+  > Demo
+`);
+
+  // Task is marked [x] in plan but has no summary file
+  writeFileSync(join(s, "S01-PLAN.md"), `# S01: Test Slice
+
+**Goal:** test
+
+## Tasks
+
+- [x] **T01: Do stuff** \`est:5m\`
+- [ ] **T02: Other stuff** \`est:5m\`
+`);
+
+  // T02 has no summary either, but it's unchecked — should be left alone
+
+  // Run doctor in diagnose mode first
+  const diagnoseReport = await runGSDDoctor(base, { fix: false });
+  const issue = diagnoseReport.issues.find(i => i.code === "task_done_missing_summary");
+  assert.ok(issue, "should detect task_done_missing_summary");
+  assert.equal(issue!.severity, "error");
+
+  // Run doctor in fix mode
+  const fixReport = await runGSDDoctor(base, { fix: true });
+  const fixApplied = fixReport.fixesApplied.some(f => f.includes("unchecked T01"));
+  assert.ok(fixApplied, "should have unchecked T01 in the fix log");
+
+  // Verify the plan now has T01 unchecked
+  const planContent = readFileSync(join(s, "S01-PLAN.md"), "utf-8");
+  assert.ok(planContent.includes("- [ ] **T01:"), "T01 should be unchecked after doctor fix");
+  assert.ok(planContent.includes("- [ ] **T02:"), "T02 should remain unchecked");
+
+  // Verify no stub summary was created
+  const stubPath = join(t, "T01-SUMMARY.md");
+  assert.ok(
+    !existsSync(stubPath),
+    "should NOT create a stub summary — task should re-execute instead",
+  );
+
+  rmSync(base, { recursive: true, force: true });
+});
+
+test("doctor does not touch task with checkbox AND summary both present", async () => {
+  const base = makeTmp("doctor-ok");
+  const gsd = join(base, ".gsd");
+  const m = join(gsd, "milestones", "M001");
+  const s = join(m, "slices", "S01");
+  const t = join(s, "tasks");
+  mkdirSync(t, { recursive: true });
+
+  writeFileSync(join(m, "M001-ROADMAP.md"), `# M001: Test
+
+## Slices
+
+- [ ] **S01: Test Slice** \`risk:low\` \`depends:[]\`
+  > Demo
+`);
+
+  writeFileSync(join(s, "S01-PLAN.md"), `# S01: Test Slice
+
+**Goal:** test
+
+## Tasks
+
+- [x] **T01: Do stuff** \`est:5m\`
+`);
+
+  writeFileSync(join(t, "T01-SUMMARY.md"), `---
+id: T01
+parent: S01
+milestone: M001
+duration: 5m
+verification_result: passed
+completed_at: 2026-01-01
+---
+
+# T01: Do stuff
+
+Done.
+`);
+
+  const report = await runGSDDoctor(base, { fix: true });
+  const hasTaskIssue = report.issues.some(i => i.code === "task_done_missing_summary");
+  assert.ok(!hasTaskIssue, "should not flag task_done_missing_summary when both exist");
+
+  // Plan should still have T01 checked
+  const planContent = readFileSync(join(s, "S01-PLAN.md"), "utf-8");
+  assert.ok(planContent.includes("- [x] **T01:"), "T01 should remain checked");
+
+  rmSync(base, { recursive: true, force: true });
+});