diff --git a/src/shared/migration.test.ts b/src/shared/migration.test.ts
index 84e563ae4..c2e6d967b 100644
--- a/src/shared/migration.test.ts
+++ b/src/shared/migration.test.ts
@@ -118,13 +118,14 @@ describe("migrateHookNames", () => {
     const hooks = ["anthropic-auto-compact", "comment-checker"]
 
     // #when: Migrate hook names
-    const { migrated, changed } = migrateHookNames(hooks)
+    const { migrated, changed, removed } = migrateHookNames(hooks)
 
     // #then: Legacy hook name should be migrated
     expect(changed).toBe(true)
     expect(migrated).toContain("anthropic-context-window-limit-recovery")
     expect(migrated).toContain("comment-checker")
     expect(migrated).not.toContain("anthropic-auto-compact")
+    expect(removed).toEqual([])
   })
 
   test("preserves current hook names unchanged", () => {
@@ -136,11 +137,12 @@ describe("migrateHookNames", () => {
     ]
 
     // #when: Migrate hook names
-    const { migrated, changed } = migrateHookNames(hooks)
+    const { migrated, changed, removed } = migrateHookNames(hooks)
 
     // #then: Current names should remain unchanged
     expect(changed).toBe(false)
     expect(migrated).toEqual(hooks)
+    expect(removed).toEqual([])
   })
 
   test("handles empty hooks array", () => {
@@ -148,11 +150,12 @@ describe("migrateHookNames", () => {
     const hooks: string[] = []
 
     // #when: Migrate hook names
-    const { migrated, changed } = migrateHookNames(hooks)
+    const { migrated, changed, removed } = migrateHookNames(hooks)
 
     // #then: Should return empty array with no changes
     expect(changed).toBe(false)
     expect(migrated).toEqual([])
+    expect(removed).toEqual([])
   })
 
   test("migrates multiple legacy hook names", () => {
@@ -166,6 +169,51 @@ describe("migrateHookNames", () => {
     expect(changed).toBe(true)
     expect(migrated).toEqual(["anthropic-context-window-limit-recovery"])
   })
+
+  test("migrates sisyphus-orchestrator to atlas", () => {
+    // #given: Config with legacy sisyphus-orchestrator hook
+    const hooks = ["sisyphus-orchestrator", "comment-checker"]
+
+    // #when: Migrate hook names
+    const { migrated, changed, removed } = migrateHookNames(hooks)
+
+    // #then: sisyphus-orchestrator should be migrated to atlas
+    expect(changed).toBe(true)
+    expect(migrated).toContain("atlas")
+    expect(migrated).toContain("comment-checker")
+    expect(migrated).not.toContain("sisyphus-orchestrator")
+    expect(removed).toEqual([])
+  })
+
+  test("removes obsolete hooks and returns them in removed array", () => {
+    // #given: Config with removed hooks from v3.0.0
+    const hooks = ["preemptive-compaction", "empty-message-sanitizer", "comment-checker"]
+
+    // #when: Migrate hook names
+    const { migrated, changed, removed } = migrateHookNames(hooks)
+
+    // #then: Removed hooks should be filtered out
+    expect(changed).toBe(true)
+    expect(migrated).toEqual(["comment-checker"])
+    expect(removed).toContain("preemptive-compaction")
+    expect(removed).toContain("empty-message-sanitizer")
+    expect(removed).toHaveLength(2)
+  })
+
+  test("handles mixed migration and removal", () => {
+    // #given: Config with both legacy rename and removed hooks
+    const hooks = ["anthropic-auto-compact", "preemptive-compaction", "sisyphus-orchestrator"]
+
+    // #when: Migrate hook names
+    const { migrated, changed, removed } = migrateHookNames(hooks)
+
+    // #then: Legacy should be renamed, removed should be filtered
+    expect(changed).toBe(true)
+    expect(migrated).toContain("anthropic-context-window-limit-recovery")
+    expect(migrated).toContain("atlas")
+    expect(migrated).not.toContain("preemptive-compaction")
+    expect(removed).toEqual(["preemptive-compaction"])
+  })
 })
 
 describe("migrateConfigFile", () => {
diff --git a/src/shared/migration.ts b/src/shared/migration.ts
index 3f9b005c8..62370d475 100644
--- a/src/shared/migration.ts
+++ b/src/shared/migration.ts
@@ -36,9 +36,15 @@ export const BUILTIN_AGENT_NAMES = new Set([
 ])
 
 // Migration map: old hook names → new hook names (for backward compatibility)
-export const HOOK_NAME_MAP: Record<string, string> = {
+// null means the hook was removed and should be filtered out from disabled_hooks
+export const HOOK_NAME_MAP: Record<string, string | null> = {
   // Legacy names (backward compatibility)
   "anthropic-auto-compact": "anthropic-context-window-limit-recovery",
+  "sisyphus-orchestrator": "atlas",
+
+  // Removed hooks (v3.0.0) - will be filtered out and user warned
+  "preemptive-compaction": null,
+  "empty-message-sanitizer": null,
 }
 
 /**
@@ -77,19 +83,28 @@ export function migrateAgentNames(agents: Record<string, unknown>): { migrated:
   return { migrated, changed }
 }
 
-export function migrateHookNames(hooks: string[]): { migrated: string[]; changed: boolean } {
+export function migrateHookNames(hooks: string[]): { migrated: string[]; changed: boolean; removed: string[] } {
   const migrated: string[] = []
+  const removed: string[] = []
   let changed = false
 
   for (const hook of hooks) {
-    const newHook = HOOK_NAME_MAP[hook] ?? hook
+    const mapping = HOOK_NAME_MAP[hook]
+
+    if (mapping === null) {
+      removed.push(hook)
+      changed = true
+      continue
+    }
+
+    const newHook = mapping ?? hook
     if (newHook !== hook) {
       changed = true
     }
     migrated.push(newHook)
   }
 
-  return { migrated, changed }
+  return { migrated, changed, removed }
 }
 
 export function migrateAgentConfigToCategory(config: Record<string, unknown>): {
@@ -167,11 +182,14 @@ export function migrateConfigFile(configPath: string, rawConfig: Record<string,
   }
 
   if (rawConfig.disabled_hooks && Array.isArray(rawConfig.disabled_hooks)) {
-    const { migrated, changed } = migrateHookNames(rawConfig.disabled_hooks as string[])
+    const { migrated, changed, removed } = migrateHookNames(rawConfig.disabled_hooks as string[])
     if (changed) {
       rawConfig.disabled_hooks = migrated
       needsWrite = true
     }
+    if (removed.length > 0) {
+      log(`Removed obsolete hooks from disabled_hooks: ${removed.join(", ")} (these hooks no longer exist in v3.0.0)`)
+    }
   }
 
   if (needsWrite) {