diff --git a/src/hooks/atlas/index.test.ts b/src/hooks/atlas/index.test.ts
index cd01eb71ae..aa28480cef 100644
--- a/src/hooks/atlas/index.test.ts
+++ b/src/hooks/atlas/index.test.ts
@@ -748,6 +748,81 @@ describe("atlas hook", () => {
         })
       })
     })
+
+    describe("Plan file transformation with autoCommit", () => {
+      const ORCHESTRATOR_SESSION = "orchestrator-plan-transform-test"
+
+      beforeEach(() => {
+        setupMessageStorage(ORCHESTRATOR_SESSION, "atlas")
+      })
+
+      afterEach(() => {
+        cleanupMessageStorage(ORCHESTRATOR_SESSION)
+      })
+
+      test("should transform Commit fields when autoCommit is false and reading plan file", async () => {
+        // given
+        const hook = createAtlasHook(createMockPluginInput(), { directory: TEST_DIR, autoCommit: false })
+        const planContent = "# Plan\n\nCommit: YES\n\n- [ ] Task 1"
+        const output = {
+          title: "Read",
+          output: planContent,
+          metadata: { filePath: "/project/.sisyphus/plans/test-plan.md" },
+        }
+
+        // when
+        await hook["tool.execute.after"](
+          { tool: "read", sessionID: ORCHESTRATOR_SESSION },
+          output
+        )
+
+        // then
+        expect(output.output).toContain("Commit: NO (user disabled auto-commits)")
+        expect(output.output).not.toContain("Commit: YES")
+      })
+
+      test("should NOT transform Commit fields when autoCommit is true", async () => {
+        // given
+        const hook = createAtlasHook(createMockPluginInput(), { directory: TEST_DIR, autoCommit: true })
+        const planContent = "# Plan\n\nCommit: YES\n\n- [ ] Task 1"
+        const output = {
+          title: "Read",
+          output: planContent,
+          metadata: { filePath: "/project/.sisyphus/plans/test-plan.md" },
+        }
+
+        // when
+        await hook["tool.execute.after"](
+          { tool: "read", sessionID: ORCHESTRATOR_SESSION },
+          output
+        )
+
+        // then
+        expect(output.output).toContain("Commit: YES")
+        expect(output.output).not.toContain("Commit: NO (user disabled auto-commits)")
+      })
+
+      test("should NOT transform when file is not a plan file", async () => {
+        // given
+        const hook = createAtlasHook(createMockPluginInput(), { directory: TEST_DIR, autoCommit: false })
+        const content = "# Regular file\n\nCommit: YES\n\nSome content"
+        const output = {
+          title: "Read",
+          output: content,
+          metadata: { filePath: "/project/src/file.ts" },
+        }
+
+        // when
+        await hook["tool.execute.after"](
+          { tool: "read", sessionID: ORCHESTRATOR_SESSION },
+          output
+        )
+
+        // then
+        expect(output.output).toContain("Commit: YES")
+        expect(output.output).not.toContain("Commit: NO (user disabled auto-commits)")
+      })
+    })
   })
 
   describe("session.idle handler (boulder continuation)", () => {
diff --git a/src/hooks/atlas/plan-commit-transform.test.ts b/src/hooks/atlas/plan-commit-transform.test.ts
new file mode 100644
index 0000000000..0c86a6a24e
--- /dev/null
+++ b/src/hooks/atlas/plan-commit-transform.test.ts
@@ -0,0 +1,156 @@
+import { describe, expect, test } from "bun:test"
+import { isPlanPath, transformPlanCommitFields } from "./plan-commit-transform"
+
+describe("isPlanPath", () => {
+  describe("#given a valid plan path", () => {
+    test("#when path is .sisyphus/plans/test.md #then returns true", () => {
+      expect(isPlanPath(".sisyphus/plans/test.md")).toBe(true)
+    })
+
+    test("#when path has full path /project/.sisyphus/plans/test.md #then returns true", () => {
+      expect(isPlanPath("/project/.sisyphus/plans/test.md")).toBe(true)
+    })
+
+    test("#when path uses backslashes #then returns true", () => {
+      expect(isPlanPath("C:\\project\\.sisyphus\\plans\\test.md")).toBe(true)
+    })
+  })
+
+  describe("#given a path with .sisyphus as substring (false-positive prevention)", () => {
+    test("#when path is foo.sisyphus-backup/plans/test.md #then returns false", () => {
+      expect(isPlanPath("foo.sisyphus-backup/plans/test.md")).toBe(false)
+    })
+
+    test("#when path is my.sisyphus/plans/test.md #then returns false", () => {
+      expect(isPlanPath("my.sisyphus/plans/test.md")).toBe(false)
+    })
+  })
+
+  describe("#given undefined or empty path", () => {
+    test("#when path is undefined #then returns false", () => {
+      expect(isPlanPath(undefined)).toBe(false)
+    })
+  })
+})
+
+describe("transformPlanCommitFields", () => {
+  describe("#given content with Commit: YES", () => {
+    test("#when transformed #then becomes Commit: NO (user disabled auto-commits)", () => {
+      const content = "Commit: YES"
+      const result = transformPlanCommitFields(content)
+      expect(result).toBe("Commit: NO (user disabled auto-commits)")
+    })
+  })
+
+  describe("#given content with Commit: NO", () => {
+    test("#when transformed #then becomes Commit: NO (user disabled auto-commits)", () => {
+      const content = "Commit: NO"
+      const result = transformPlanCommitFields(content)
+      expect(result).toBe("Commit: NO (user disabled auto-commits)")
+    })
+  })
+
+  describe("#given content with Commit fields with extra whitespace", () => {
+    test("#when transformed #then handles whitespace variations", () => {
+      const content = "Commit:   YES"
+      const result = transformPlanCommitFields(content)
+      expect(result).toBe("Commit: NO (user disabled auto-commits)")
+    })
+  })
+
+  describe("#given content with multiple Commit fields", () => {
+    test("#when transformed #then all Commit fields are transformed", () => {
+      const content = `
+## Task 1
+Commit: YES
+
+## Task 2
+Commit: NO
+
+## Task 3
+Commit: YES
+`
+      const result = transformPlanCommitFields(content)
+      expect(result).toBe(`
+## Task 1
+Commit: NO (user disabled auto-commits)
+
+## Task 2
+Commit: NO (user disabled auto-commits)
+
+## Task 3
+Commit: NO (user disabled auto-commits)
+`)
+    })
+  })
+
+  describe("#given content with ReCommit: YES (word boundary check)", () => {
+    test("#when transformed #then ReCommit is NOT transformed", () => {
+      const content = "ReCommit: YES"
+      const result = transformPlanCommitFields(content)
+      expect(result).toBe("ReCommit: YES")
+    })
+  })
+
+  describe("#given content without Commit fields", () => {
+    test("#when transformed #then content is unchanged", () => {
+      const content = `
+## Task
+- [ ] Do something
+- [ ] Do another thing
+`
+      const result = transformPlanCommitFields(content)
+      expect(result).toBe(content)
+    })
+  })
+
+  describe("#given already transformed content", () => {
+    test("#when transformed again #then remains idempotent", () => {
+      const originalContent = "Commit: YES"
+      const firstTransform = transformPlanCommitFields(originalContent)
+      const secondTransform = transformPlanCommitFields(firstTransform)
+      expect(secondTransform).toBe(firstTransform)
+      expect(secondTransform).toBe("Commit: NO (user disabled auto-commits)")
+    })
+  })
+
+  describe("#given complex plan content with mixed fields", () => {
+    test("#when transformed #then only Commit fields are changed", () => {
+      const content = `
+# Plan
+
+## 1. TASK
+Some task description
+
+## 2. EXPECTED OUTCOME
+- [ ] Files created
+- [ ] Tests pass
+
+## 3. REQUIRED TOOLS
+- Write
+- Bash
+
+## 4. Commit: YES
+This should be committed after completion.
+`
+      const result = transformPlanCommitFields(content)
+      expect(result).toBe(`
+# Plan
+
+## 1. TASK
+Some task description
+
+## 2. EXPECTED OUTCOME
+- [ ] Files created
+- [ ] Tests pass
+
+## 3. REQUIRED TOOLS
+- Write
+- Bash
+
+## 4. Commit: NO (user disabled auto-commits)
+This should be committed after completion.
+`)
+    })
+  })
+})
diff --git a/src/hooks/atlas/plan-commit-transform.ts b/src/hooks/atlas/plan-commit-transform.ts
new file mode 100644
index 0000000000..f615bb4592
--- /dev/null
+++ b/src/hooks/atlas/plan-commit-transform.ts
@@ -0,0 +1,11 @@
+export function isPlanPath(filePath: string | undefined): boolean {
+  if (!filePath) return false
+  return /(^|[/\\])\.sisyphus[/\\]plans[/\\].*\.md$/.test(filePath)
+}
+
+/**
+ * Uses negative lookahead to ensure idempotency (won't re-transform already-transformed content).
+ */
+export function transformPlanCommitFields(content: string): string {
+  return content.replace(/\bCommit:\s*(YES|NO)(?!\s*\(user disabled auto-commits\))/g, "Commit: NO (user disabled auto-commits)")
+}
diff --git a/src/hooks/atlas/tool-execute-after.ts b/src/hooks/atlas/tool-execute-after.ts
index fd8c1824cd..e8dee49c02 100644
--- a/src/hooks/atlas/tool-execute-after.ts
+++ b/src/hooks/atlas/tool-execute-after.ts
@@ -9,8 +9,29 @@ import { isSisyphusPath } from "./sisyphus-path"
 import { extractSessionIdFromOutput } from "./subagent-session-id"
 import { buildCompletionGate, buildOrchestratorReminder, buildStandaloneVerificationReminder } from "./verification-reminders"
 import { isWriteOrEditToolName } from "./write-edit-tool-policy"
+import { isPlanPath, transformPlanCommitFields } from "./plan-commit-transform"
 import type { ToolExecuteAfterInput, ToolExecuteAfterOutput } from "./types"
 
+/**
+ * Extract file path from metadata using multiple possible key names.
+ * Tries: filepath, filePath, path, file (in that order)
+ */
+function extractFilePath(metadata: unknown): string | undefined {
+  if (!metadata || typeof metadata !== "object") {
+    return undefined
+  }
+
+  const objectMeta = metadata as Record<string, unknown>
+  const candidates = [objectMeta.filepath, objectMeta.filePath, objectMeta.path, objectMeta.file]
+  for (const candidate of candidates) {
+    if (typeof candidate === "string" && candidate.length > 0) {
+      return candidate
+    }
+  }
+
+  return undefined
+}
+
 export function createToolExecuteAfterHandler(input: {
   ctx: PluginInput
   pendingFilePaths: Map<string, string>
@@ -18,7 +39,6 @@ export function createToolExecuteAfterHandler(input: {
   }): (toolInput: ToolExecuteAfterInput, toolOutput: ToolExecuteAfterOutput) => Promise<void> {
   const { ctx, pendingFilePaths, autoCommit } = input
   return async (toolInput, toolOutput): Promise<void> => {
-    // Guard against undefined output (e.g., from /review command - see issue #1035)
     if (!toolOutput) {
       return
     }
@@ -28,9 +48,12 @@ export function createToolExecuteAfterHandler(input: {
     }
 
     if (isWriteOrEditToolName(toolInput.tool)) {
-      let filePath = toolInput.callID ? pendingFilePaths.get(toolInput.callID) : undefined
-      if (toolInput.callID) {
-        pendingFilePaths.delete(toolInput.callID)
+      const mapKey = toolInput.sessionID && toolInput.callID
+        ? `${toolInput.sessionID}:${toolInput.callID}`
+        : toolInput.callID
+      let filePath = mapKey ? pendingFilePaths.get(mapKey) : undefined
+      if (mapKey) {
+        pendingFilePaths.delete(mapKey)
       }
       if (!filePath) {
         filePath = toolOutput.metadata?.filePath as string | undefined
@@ -46,6 +69,32 @@ export function createToolExecuteAfterHandler(input: {
       return
     }
 
+    if (toolInput.tool === "read" || toolInput.tool === "Read") {
+      // Always cleanup pendingFilePaths to prevent memory leak
+      const mapKey = toolInput.sessionID && toolInput.callID
+        ? `${toolInput.sessionID}:${toolInput.callID}`
+        : toolInput.callID
+      let filePath = mapKey ? pendingFilePaths.get(mapKey) : undefined
+      if (mapKey) {
+        pendingFilePaths.delete(mapKey)
+      }
+      if (!filePath) {
+        filePath = extractFilePath(toolOutput.metadata)
+      }
+      // Transform plan files only when autoCommit is disabled
+      if (!autoCommit && filePath && isPlanPath(filePath)) {
+        const output = toolOutput.output
+        if (output && typeof output === "string") {
+          toolOutput.output = transformPlanCommitFields(output)
+          log(`[${HOOK_NAME}] Transformed plan Commit fields for read`, {
+            sessionID: toolInput.sessionID,
+            filePath,
+          })
+        }
+      }
+      return
+    }
+
     if (toolInput.tool !== "task") {
       return
     }
diff --git a/src/hooks/atlas/tool-execute-before.ts b/src/hooks/atlas/tool-execute-before.ts
index 51f670000b..e188d30f6a 100644
--- a/src/hooks/atlas/tool-execute-before.ts
+++ b/src/hooks/atlas/tool-execute-before.ts
@@ -27,8 +27,8 @@ export function createToolExecuteBeforeHandler(input: {
       const filePath = (toolOutput.args.filePath ?? toolOutput.args.path ?? toolOutput.args.file) as string | undefined
       if (filePath && !isSisyphusPath(filePath)) {
         // Store filePath for use in tool.execute.after
-        if (toolInput.callID) {
-          pendingFilePaths.set(toolInput.callID, filePath)
+        if (toolInput.callID && toolInput.sessionID) {
+          pendingFilePaths.set(`${toolInput.sessionID}:${toolInput.callID}`, filePath)
         }
         const warning = ORCHESTRATOR_DELEGATION_REQUIRED.replace("$FILE_PATH", filePath)
         toolOutput.message = (toolOutput.message || "") + warning
@@ -41,6 +41,15 @@ export function createToolExecuteBeforeHandler(input: {
       return
     }
 
+    // Store filePath for Read tools (for plan transformation in tool.execute.after)
+    if (toolInput.tool === "read" || toolInput.tool === "Read") {
+      const filePath = (toolOutput.args.filePath ?? toolOutput.args.path ?? toolOutput.args.file) as string | undefined
+      if (filePath && toolInput.callID && toolInput.sessionID) {
+        pendingFilePaths.set(`${toolInput.sessionID}:${toolInput.callID}`, filePath)
+      }
+      return
+    }
+
     // Check task - inject single-task directive
     if (toolInput.tool === "task") {
       const prompt = toolOutput.args.prompt as string | undefined
@@ -50,6 +59,7 @@ export function createToolExecuteBeforeHandler(input: {
           sessionID: toolInput.sessionID,
         })
       }
+      return
     }
   }
 }
diff --git a/src/hooks/atlas/verification-reminders.ts b/src/hooks/atlas/verification-reminders.ts
index 019e5e8699..e6dda221fc 100644
--- a/src/hooks/atlas/verification-reminders.ts
+++ b/src/hooks/atlas/verification-reminders.ts
@@ -57,9 +57,19 @@ export function buildOrchestratorReminder(
 - Stage ONLY the verified changes
 - Commit with clear message describing what was done
 `
-    : ""
+    : `
+**STEP 7: COMMITS DISABLED**
 
-  const nextStepNumber = autoCommit ? 8 : 7
+The user has disabled auto-commits (\`start_work.auto_commit: false\`).
+Changes will NOT be committed automatically.
+
+**IMPORTANT: Inform the user now:**
+- State clearly that no commits were made
+- Summarize what changes were completed
+- Ask if they want to commit manually or enable auto-commit
+`
+
+  const nextStepNumber = 8
 
   return `
 ---