diff --git a/.changeset/calm-herons-wake.md b/.changeset/calm-herons-wake.md
new file mode 100644
index 000000000..ede0fe87f
--- /dev/null
+++ b/.changeset/calm-herons-wake.md
@@ -0,0 +1,5 @@
+---
+type: Fixed
+pr: 3272
+---
+**`gsd-sdk query milestone.complete --help` (and all mutating query handlers) no longer execute mutations** — the dispatcher now short-circuits to a non-mutating help stub when `--help`/`-h` appears in args for any native mutating handler (dispatcher-level guard, fail-closed by default). `milestoneComplete` also rejects `--help`/`-h` as a version value before any disk write (handler-level defense-in-depth).
diff --git a/sdk/src/query/phase-lifecycle.test.ts b/sdk/src/query/phase-lifecycle.test.ts
index 92eb01222..7e85d0d10 100644
--- a/sdk/src/query/phase-lifecycle.test.ts
+++ b/sdk/src/query/phase-lifecycle.test.ts
@@ -1505,6 +1505,68 @@ describe('phasesArchive', () => {
   });
 });
 
+// ─── milestoneComplete help-flag defense (#3259) ────────────────────────────
+
+describe('milestoneComplete help-flag defense', () => {
+  it('rejects --help as a version value with GSDError before any disk write', async () => {
+    const { milestoneComplete } = await import('./phase-lifecycle.js');
+    const { GSDError, ErrorClassification } = await import('../errors.js');
+    await setupTestProject(tmpDir);
+
+    // Capture pre-invocation filesystem state
+    const planningDir = join(tmpDir, '.planning');
+    const milestonesPath = join(planningDir, 'MILESTONES.md');
+    const statePath = join(planningDir, 'STATE.md');
+    const preStateStat = await import('node:fs').then((m) => m.statSync(statePath));
+    const milestonesExistedBefore = existsSync(milestonesPath);
+
+    let thrown: unknown;
+    try {
+      await milestoneComplete(['--help'], tmpDir);
+    } catch (e) {
+      thrown = e;
+    }
+
+    expect(thrown).toBeInstanceOf(GSDError);
+    const err = thrown as InstanceType<typeof GSDError>;
+    expect(err.classification).toBe(ErrorClassification.Validation);
+    expect(err.message).toContain('--help');
+
+    // Assert no files were written
+    const postStateStat = await import('node:fs').then((m) => m.statSync(statePath));
+    expect(postStateStat.mtimeMs).toBe(preStateStat.mtimeMs);
+    expect(existsSync(milestonesPath)).toBe(milestonesExistedBefore);
+  });
+
+  it('rejects -h as a version value with GSDError before any disk write', async () => {
+    const { milestoneComplete } = await import('./phase-lifecycle.js');
+    const { GSDError, ErrorClassification } = await import('../errors.js');
+    await setupTestProject(tmpDir);
+
+    const statePath = join(tmpDir, '.planning', 'STATE.md');
+    const preStateStat = await import('node:fs').then((m) => m.statSync(statePath));
+    const milestonesPath = join(tmpDir, '.planning', 'MILESTONES.md');
+    const milestonesExistedBefore = existsSync(milestonesPath);
+
+    let thrown: unknown;
+    try {
+      await milestoneComplete(['-h'], tmpDir);
+    } catch (e) {
+      thrown = e;
+    }
+
+    expect(thrown).toBeInstanceOf(GSDError);
+    const err = thrown as InstanceType<typeof GSDError>;
+    expect(err.classification).toBe(ErrorClassification.Validation);
+    expect(err.message).toContain('-h');
+
+    // Assert no files were written
+    const postStateStat = await import('node:fs').then((m) => m.statSync(statePath));
+    expect(postStateStat.mtimeMs).toBe(preStateStat.mtimeMs);
+    expect(existsSync(milestonesPath)).toBe(milestonesExistedBefore);
+  });
+});
+
 // ─── Registry integration ──────────────────────────────────────────────────
 
 describe('lifecycle handlers in registry', () => {
diff --git a/sdk/src/query/phase-lifecycle.ts b/sdk/src/query/phase-lifecycle.ts
index b07bbe196..cae5c81d9 100644
--- a/sdk/src/query/phase-lifecycle.ts
+++ b/sdk/src/query/phase-lifecycle.ts
@@ -1781,6 +1781,14 @@ export const milestoneComplete: QueryHandler = async (args, projectDir, workstre
   if (!version) {
     throw new GSDError('version required for milestone complete (e.g., v1.0)', ErrorClassification.Validation);
   }
+  // #3259: defense-in-depth — reject --help / -h as a version value before
+  // any disk write, regardless of whether the dispatcher guard intercepted first.
+  if (version === '--help' || version === '-h') {
+    throw new GSDError(
+      `"${version}" is not a valid milestone version; see \`gsd-sdk query --help\` for command list`,
+      ErrorClassification.Validation,
+    );
+  }
   assertNoNullBytes(version, 'version');
 
   const nameOpt = parseMultiwordArg(args, 'name');
diff --git a/sdk/src/query/query-dispatch.test.ts b/sdk/src/query/query-dispatch.test.ts
index 01ccbf9a1..70b22d72e 100644
--- a/sdk/src/query/query-dispatch.test.ts
+++ b/sdk/src/query/query-dispatch.test.ts
@@ -1,11 +1,13 @@
 import { describe, it, expect, beforeEach, afterEach } from 'vitest';
-import { mkdir, rm, writeFile } from 'node:fs/promises';
+import { mkdir, rm, writeFile, readdir, stat } from 'node:fs/promises';
 import { join } from 'node:path';
 import { tmpdir } from 'node:os';
+import { existsSync } from 'node:fs';
 import { createRegistry } from './index.js';
 import { GSDToolsError } from '../gsd-tools-error.js';
 import { runQueryDispatch } from './query-dispatch.js';
 import { createCommandTopology } from './command-topology.js';
+import { COMMAND_MUTATION_SET } from './command-definition.js';
 describe('runQueryDispatch', () => {
   let tmpDir: string;
   let fixtureDir: string;
@@ -188,3 +190,210 @@ describe('runQueryDispatch', () => {
     expect(out.error.details).toMatchObject({ command: 'state.json', args: [] });
   });
 });
+
+// ─── #3259 help-flag non-mutating guard ──────────────────────────────────────
+
+describe('--help guard: dispatcher short-circuits mutating native handlers', () => {
+  let tmpDir: string;
+
+  beforeEach(async () => {
+    tmpDir = join(tmpdir(), `qdispatch-help-${Date.now()}-${Math.random().toString(36).slice(2)}`);
+    await mkdir(join(tmpDir, '.planning', 'phases'), { recursive: true });
+    // Minimal fixture required for most handlers to not crash on fs reads
+    await writeFile(join(tmpDir, '.planning', 'ROADMAP.md'), '# Roadmap\n\n## Current Milestone: v1.0\n', 'utf-8');
+    await writeFile(
+      join(tmpDir, '.planning', 'STATE.md'),
+      '---\ngsd_state_version: 1.0\nmilestone: v1.0\nstatus: executing\n---\n\n# Project State\n',
+      'utf-8',
+    );
+    await writeFile(
+      join(tmpDir, '.planning', 'config.json'),
+      JSON.stringify({ model_profile: 'balanced', phase_naming: 'sequential' }),
+      'utf-8',
+    );
+  });
+
+  afterEach(async () => {
+    await rm(tmpDir, { recursive: true, force: true });
+  });
+
+  /**
+   * Collect a digest of all file mtimes under .planning/ so we can compare
+   * pre- and post-invocation state without reading file content.
+   */
+  async function collectPlanningDigest(projectDir: string): Promise<Map<string, number>> {
+    const planningDir = join(projectDir, '.planning');
+    const digest = new Map<string, number>();
+    async function walk(dir: string): Promise<void> {
+      let entries;
+      try {
+        entries = await readdir(dir, { withFileTypes: true });
+      } catch {
+        return;
+      }
+      for (const entry of entries) {
+        const full = join(dir, entry.name);
+        if (entry.isDirectory()) {
+          await walk(full);
+        } else {
+          try {
+            const s = await stat(full);
+            digest.set(full, s.mtimeMs);
+          } catch {
+            /* ignore */
+          }
+        }
+      }
+    }
+    await walk(planningDir);
+    return digest;
+  }
+
+  it('milestone.complete --help returns non-mutating help stub without writing to .planning/', async () => {
+    const registry = createRegistry();
+    const topology = createCommandTopology(registry);
+
+    const preDig = await collectPlanningDigest(tmpDir);
+
+    const out = await runQueryDispatch({
+      registry,
+      projectDir: tmpDir,
+      cjsFallbackEnabled: false,
+      resolveGsdToolsPath: () => '',
+      topology,
+    }, ['milestone.complete', '--help']);
+
+    expect(out.ok).toBe(true);
+    if (!out.ok) throw new Error('expected success');
+
+    // Response must contain help stub, not a milestone record
+    const parsed = JSON.parse(out.stdout) as Record<string, unknown>;
+    expect(typeof parsed.help).toBe('string');
+    expect(parsed.help).toContain('milestone.complete');
+
+    // .planning/ directory must be byte-identical (no new or modified files)
+    const postDig = await collectPlanningDigest(tmpDir);
+    expect(postDig.size).toBe(preDig.size);
+    for (const [path, mtime] of preDig) {
+      expect(postDig.get(path)).toBe(mtime);
+    }
+    // MILESTONES.md must not have been created
+    expect(existsSync(join(tmpDir, '.planning', 'MILESTONES.md'))).toBe(false);
+  });
+
+  it('milestone.complete -h returns non-mutating help stub without writing to .planning/', async () => {
+    const registry = createRegistry();
+    const topology = createCommandTopology(registry);
+
+    const preDig = await collectPlanningDigest(tmpDir);
+
+    const out = await runQueryDispatch({
+      registry,
+      projectDir: tmpDir,
+      cjsFallbackEnabled: false,
+      resolveGsdToolsPath: () => '',
+      topology,
+    }, ['milestone.complete', '-h']);
+
+    expect(out.ok).toBe(true);
+    if (!out.ok) throw new Error('expected success');
+
+    const parsed = JSON.parse(out.stdout) as Record<string, unknown>;
+    expect(typeof parsed.help).toBe('string');
+
+    const postDig = await collectPlanningDigest(tmpDir);
+    expect(postDig.size).toBe(preDig.size);
+    for (const [path, mtime] of preDig) {
+      expect(postDig.get(path)).toBe(mtime);
+    }
+  });
+
+  it('registry-driven: all native mutating handlers with --help do not modify .planning/', async () => {
+    const registry = createRegistry();
+    const topology = createCommandTopology(registry);
+
+    // Collect all registered mutating commands from the manifest
+    const mutatingCommands = Array.from(COMMAND_MUTATION_SET).filter((cmd) => {
+      // Only canonical forms that are registered in the registry (not aliases)
+      return registry.has(cmd);
+    });
+
+    for (const cmd of mutatingCommands) {
+      // Reset fixture between each command to ensure isolation
+      await rm(join(tmpDir, '.planning'), { recursive: true, force: true });
+      await mkdir(join(tmpDir, '.planning', 'phases'), { recursive: true });
+      await writeFile(join(tmpDir, '.planning', 'ROADMAP.md'), '# Roadmap\n\n## Current Milestone: v1.0\n', 'utf-8');
+      await writeFile(
+        join(tmpDir, '.planning', 'STATE.md'),
+        '---\ngsd_state_version: 1.0\nmilestone: v1.0\nstatus: executing\n---\n\n# Project State\n',
+        'utf-8',
+      );
+      await writeFile(
+        join(tmpDir, '.planning', 'config.json'),
+        JSON.stringify({ model_profile: 'balanced', phase_naming: 'sequential' }),
+        'utf-8',
+      );
+
+      const preDig = await collectPlanningDigest(tmpDir);
+
+      // Invoke via dispatcher with --help in args (after the command token)
+      // argv format: [cmd, '--help'] where cmd may be dotted or spaced
+      const argv = [...cmd.split(' '), '--help'];
+      const out = await runQueryDispatch({
+        registry,
+        projectDir: tmpDir,
+        cjsFallbackEnabled: false,
+        resolveGsdToolsPath: () => '',
+        topology,
+      }, argv);
+
+      // Must succeed (help stub) or fail for validation reasons (e.g. arg rewriting
+      // that produces a non-mutating command) — the invariant is no disk mutation.
+      const postDig = await collectPlanningDigest(tmpDir);
+      expect(postDig.size, `${cmd} --help created new .planning files`).toBe(preDig.size);
+      for (const [path, mtime] of preDig) {
+        expect(postDig.get(path), `${cmd} --help modified ${path}`).toBe(mtime);
+      }
+    }
+  });
+
+  it('preserves #3019 contract: unknown-cmd --help falls through to cjs (not intercepted by guard)', async () => {
+    // The guard only fires when a NATIVE MUTATING handler is matched.
+    // Unknown commands with --help must still fall through to CJS fallback.
+    const script = await (async () => {
+      const scriptPath = join(tmpDir, 'text.cjs');
+      await writeFile(scriptPath, "process.stdout.write('USAGE: help text');", { mode: 0o755 });
+      return scriptPath;
+    })();
+
+    const registry = createRegistry();
+    const out = await runQueryDispatch({
+      registry,
+      projectDir: tmpDir,
+      cjsFallbackEnabled: true,
+      resolveGsdToolsPath: () => script,
+      topology: createCommandTopology(registry),
+    }, ['unknown-cmd', '--help']);
+
+    expect(out.ok).toBe(true);
+    if (!out.ok) throw new Error('expected success');
+    expect(out.stdout).toBe('USAGE: help text\n');
+  });
+
+  it('non-mutating native handlers are unaffected when --help is in args', async () => {
+    // E.g. state.json is non-mutating; --help in args should still dispatch normally.
+    const registry = createRegistry();
+    const out = await runQueryDispatch({
+      registry,
+      projectDir: tmpDir,
+      cjsFallbackEnabled: true,
+      resolveGsdToolsPath: () => '',
+      dispatchNative: async () => ({ data: { ok: true } }),
+      topology: createCommandTopology(registry),
+    }, ['state', 'json', '--help']);
+
+    // state.json is non-mutating, so --help should pass through to the handler
+    // The mock handler returns successfully, so we get a success result.
+    expect(out.ok).toBe(true);
+  });
+});
diff --git a/sdk/src/query/query-dispatch.ts b/sdk/src/query/query-dispatch.ts
index 5f38a6ec9..42d7a0384 100644
--- a/sdk/src/query/query-dispatch.ts
+++ b/sdk/src/query/query-dispatch.ts
@@ -213,6 +213,21 @@ export async function runQueryDispatch(deps: QueryDispatchDeps, queryArgv: strin
     return toDispatchFailure(mapFallbackDispatchError(new Error('No native match in dispatch plan'), normCmd, normArgs));
   }
 
+  // #3259: guard — if the invocation contains --help / -h AND the matched
+  // handler is a mutating command (mutation: true in the command manifest),
+  // short-circuit to a non-mutating stub. Mutating handlers are not help-aware
+  // by default (fail-closed). This prevents e.g. `milestone.complete --help`
+  // from writing milestone artifacts to disk.
+  const helpFlagPresent = matched.args.some((a) => a === '--help' || a === '-h');
+  if (helpFlagPresent && matched.mutation) {
+    return dispatchSuccess(
+      formatSuccess(
+        { help: `Usage: gsd-sdk query ${matched.canonical} [args...]` },
+        undefined,
+      ),
+    );
+  }
+
   const dispatchNative = deps.nativeAdapter
     ? (cmd: string, args: string[]) => deps.nativeAdapter!.dispatch(cmd, args)
     : deps.dispatchNative;