diff --git a/get-shit-done/bin/lib/init.cjs b/get-shit-done/bin/lib/init.cjs
index a092ffa27..214baa2ba 100644
--- a/get-shit-done/bin/lib/init.cjs
+++ b/get-shit-done/bin/lib/init.cjs
@@ -1104,7 +1104,9 @@ function cmdInitManager(cwd, raw) {
     return true;
   });
 
-  const completedCount = phases.filter(p => p.disk_status === 'complete').length;
+  // Exclude backlog phases (999.x) from completion accounting (#2129)
+  const nonBacklogPhases = phases.filter(p => !/^999(?:\.|$)/.test(p.number));
+  const completedCount = nonBacklogPhases.filter(p => p.disk_status === 'complete').length;
 
   // Read manager flags from config (passthrough flags for each step)
   // Validate: flags must be CLI-safe (only --flags, alphanumeric, hyphens, spaces)
@@ -1135,7 +1137,7 @@ function cmdInitManager(cwd, raw) {
     in_progress_count: phases.filter(p => ['partial', 'planned', 'discussed', 'researched'].includes(p.disk_status)).length,
     recommended_actions: filteredActions,
     waiting_signal: waitingSignal,
-    all_complete: completedCount === phases.length && phases.length > 0,
+    all_complete: completedCount === nonBacklogPhases.length && nonBacklogPhases.length > 0,
     project_exists: pathExistsInternal(cwd, '.planning/PROJECT.md'),
     roadmap_exists: true,
     state_exists: true,
diff --git a/get-shit-done/bin/lib/phase.cjs b/get-shit-done/bin/lib/phase.cjs
index 3e8450bfc..9bdf70e8c 100644
--- a/get-shit-done/bin/lib/phase.cjs
+++ b/get-shit-done/bin/lib/phase.cjs
@@ -838,9 +838,11 @@ function cmdPhaseComplete(cwd, phaseNum, raw) {
       .sort((a, b) => comparePhaseNum(a, b));
 
     // Find the next phase directory after current
+    // Skip backlog phases (999.x) — they are parked ideas, not sequential work (#2129)
     for (const dir of dirs) {
       const dm = dir.match(/^(\d+[A-Z]?(?:\.\d+)*)-?(.*)/i);
       if (dm) {
+        if (/^999(?:\.|$)/.test(dm[1])) continue;
         if (comparePhaseNum(dm[1], phaseNum) > 0) {
           nextPhaseNum = dm[1];
           nextPhaseName = dm[2] || null;
diff --git a/tests/init-manager.test.cjs b/tests/init-manager.test.cjs
index 1c6d5cb39..8f1d37794 100644
--- a/tests/init-manager.test.cjs
+++ b/tests/init-manager.test.cjs
@@ -531,4 +531,46 @@ describe('init manager', () => {
 
     assert.strictEqual(output.response_language, undefined);
   });
+
+  test('all_complete is true when non-backlog phases are complete and 999.x exists (#2129)', () => {
+    writeState(tmpDir);
+    writeRoadmap(tmpDir, [
+      { number: '1', name: 'Setup', complete: true },
+      { number: '2', name: 'Core', complete: true },
+      { number: '3', name: 'Polish', complete: true },
+      { number: '999.1', name: 'Backlog idea' },
+    ]);
+
+    // Scaffold completed phases on disk
+    scaffoldPhase(tmpDir, 1, { slug: 'setup', plans: 2, summaries: 2 });
+    scaffoldPhase(tmpDir, 2, { slug: 'core', plans: 1, summaries: 1 });
+    scaffoldPhase(tmpDir, 3, { slug: 'polish', plans: 1, summaries: 1 });
+
+    const result = runGsdTools('init manager', tmpDir);
+    assert.ok(result.success, `Command failed: ${result.error}`);
+
+    const output = JSON.parse(result.output);
+    assert.strictEqual(output.all_complete, true, 'all_complete should be true when only 999.x phases remain incomplete');
+  });
+
+  test('all_complete false with incomplete non-backlog phase still produces recommended_actions (#2129)', () => {
+    writeState(tmpDir);
+    writeRoadmap(tmpDir, [
+      { number: '1', name: 'Setup', complete: true },
+      { number: '2', name: 'Core', complete: true },
+      { number: '3', name: 'Polish' },
+      { number: '999.1', name: 'Backlog idea' },
+    ]);
+
+    scaffoldPhase(tmpDir, 1, { slug: 'setup', plans: 1, summaries: 1 });
+    scaffoldPhase(tmpDir, 2, { slug: 'core', plans: 1, summaries: 1 });
+    // Phase 3 has no directory — should trigger discuss recommendation
+
+    const result = runGsdTools('init manager', tmpDir);
+    assert.ok(result.success, `Command failed: ${result.error}`);
+
+    const output = JSON.parse(result.output);
+    assert.strictEqual(output.all_complete, false, 'all_complete should be false with phase 3 incomplete');
+    assert.ok(output.recommended_actions.length > 0, 'recommended_actions should not be empty when non-backlog phases remain');
+  });
 });
diff --git a/tests/phase.test.cjs b/tests/phase.test.cjs
index 338fb2596..b23b31cad 100644
--- a/tests/phase.test.cjs
+++ b/tests/phase.test.cjs
@@ -2330,6 +2330,83 @@ describe('phase complete updates Performance Metrics', () => {
   });
 });
 
+// ─────────────────────────────────────────────────────────────────────────────
+// phase complete — backlog phase (999.x) exclusion (#2129)
+// ─────────────────────────────────────────────────────────────────────────────
+
+describe('phase complete excludes 999.x backlog from next-phase (#2129)', () => {
+  let tmpDir;
+
+  beforeEach(() => {
+    tmpDir = createTempProject();
+  });
+
+  afterEach(() => {
+    cleanup(tmpDir);
+  });
+
+  test('next phase skips 999.x backlog dirs and falls back to roadmap', () => {
+    // ROADMAP defines phases 1, 2, 3 and a backlog 999.1
+    fs.writeFileSync(
+      path.join(tmpDir, '.planning', 'ROADMAP.md'),
+      [
+        '# Roadmap',
+        '',
+        '- [ ] Phase 1: Setup',
+        '- [ ] Phase 2: Core',
+        '- [ ] Phase 3: Polish',
+        '- [ ] Phase 999.1: Backlog idea',
+        '',
+        '### Phase 1: Setup',
+        '**Goal:** Initial setup',
+        '',
+        '### Phase 2: Core',
+        '**Goal:** Build core',
+        '',
+        '### Phase 3: Polish',
+        '**Goal:** Polish everything',
+        '',
+        '### Phase 999.1: Backlog idea',
+        '**Goal:** Parked idea',
+      ].join('\n')
+    );
+    fs.writeFileSync(
+      path.join(tmpDir, '.planning', 'STATE.md'),
+      [
+        '# State',
+        '',
+        '**Current Phase:** 02',
+        '**Status:** In progress',
+        '**Current Plan:** 02-01',
+        '**Last Activity:** 2025-01-01',
+        '**Last Activity Description:** Working',
+      ].join('\n')
+    );
+
+    // Phase 1 and 2 exist on disk, phase 3 does NOT exist yet, 999.1 DOES exist
+    const p1 = path.join(tmpDir, '.planning', 'phases', '01-setup');
+    fs.mkdirSync(p1, { recursive: true });
+    fs.writeFileSync(path.join(p1, '01-01-PLAN.md'), '# Plan');
+    fs.writeFileSync(path.join(p1, '01-01-SUMMARY.md'), '# Summary');
+
+    const p2 = path.join(tmpDir, '.planning', 'phases', '02-core');
+    fs.mkdirSync(p2, { recursive: true });
+    fs.writeFileSync(path.join(p2, '02-01-PLAN.md'), '# Plan');
+    fs.writeFileSync(path.join(p2, '02-01-SUMMARY.md'), '# Summary');
+
+    // Backlog stub on disk — this is what triggers the bug
+    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '999.1-backlog-idea'), { recursive: true });
+
+    const result = runGsdTools('phase complete 2', tmpDir);
+    assert.ok(result.success, `Command failed: ${result.error}`);
+
+    const output = JSON.parse(result.output);
+    // Should find phase 3 from roadmap, NOT 999.1 from filesystem
+    assert.strictEqual(output.next_phase, '3', 'next_phase should be 3, not 999.1');
+    assert.strictEqual(output.is_last_phase, false, 'should not be last phase');
+  });
+});
+
 // ─────────────────────────────────────────────────────────────────────────────
 // milestone complete command
 // ─────────────────────────────────────────────────────────────────────────────