diff --git a/src/cli/doctor/formatter.test.ts b/src/cli/doctor/formatter.test.ts
index 5884997af..e0c280995 100644
--- a/src/cli/doctor/formatter.test.ts
+++ b/src/cli/doctor/formatter.test.ts
@@ -1,6 +1,10 @@
-import { afterEach, describe, expect, it, mock } from "bun:test"
+import { afterEach, afterAll, describe, expect, it, mock } from "bun:test"
 import type { DoctorResult } from "./types"
 
+const realFormatDefault = await import("./format-default")
+const realFormatStatus = await import("./format-status")
+const realFormatVerbose = await import("./format-verbose")
+
 function createDoctorResult(): DoctorResult {
   return {
     results: [
@@ -44,6 +48,12 @@ describe("formatter", () => {
     mock.restore()
   })
 
+  afterAll(() => {
+    mock.module("./format-default", () => ({ ...realFormatDefault }))
+    mock.module("./format-status", () => ({ ...realFormatStatus }))
+    mock.module("./format-verbose", () => ({ ...realFormatVerbose }))
+  })
+
   describe("formatDoctorOutput", () => {
     it("dispatches to default formatter for default mode", async () => {
       //#given
diff --git a/src/cli/doctor/runner.test.ts b/src/cli/doctor/runner.test.ts
index ca96b0794..e2070d1cc 100644
--- a/src/cli/doctor/runner.test.ts
+++ b/src/cli/doctor/runner.test.ts
@@ -1,6 +1,9 @@
-import { afterEach, describe, expect, it, mock } from "bun:test"
+import { afterEach, afterAll, describe, expect, it, mock } from "bun:test"
 import type { CheckDefinition, CheckResult, DoctorResult, SystemInfo, ToolsSummary } from "./types"
 
+const realChecks = await import("./checks")
+const realFormatter = await import("./formatter")
+
 function createSystemInfo(): SystemInfo {
   return {
     opencodeVersion: "1.0.200",
@@ -47,6 +50,11 @@ describe("runner", () => {
     mock.restore()
   })
 
+  afterAll(() => {
+    mock.module("./checks", () => ({ ...realChecks }))
+    mock.module("./formatter", () => ({ ...realFormatter }))
+  })
+
   describe("runCheck", () => {
     it("returns fail result with issue when check throws", async () => {
       //#given
diff --git a/src/cli/mcp-oauth/login.test.ts b/src/cli/mcp-oauth/login.test.ts
index 917652f76..6d9998a1e 100644
--- a/src/cli/mcp-oauth/login.test.ts
+++ b/src/cli/mcp-oauth/login.test.ts
@@ -1,4 +1,6 @@
-import { describe, it, expect, beforeEach, afterEach, mock } from "bun:test"
+import { describe, it, expect, beforeEach, afterEach, afterAll, mock } from "bun:test"
+
+const realMcpOauthProvider = await import("../../features/mcp-oauth/provider")
 
 const mockLogin = mock(() => Promise.resolve({ accessToken: "test-token", expiresAt: 1710000000 }))
 
@@ -11,6 +13,10 @@ mock.module("../../features/mcp-oauth/provider", () => ({
   },
 }))
 
+afterAll(() => {
+  mock.module("../../features/mcp-oauth/provider", () => ({ ...realMcpOauthProvider }))
+})
+
 const { login } = await import("./login")
 
 describe("login command", () => {
diff --git a/src/cli/run/integration.test.ts b/src/cli/run/integration.test.ts
index 1cbfa0847..c38e72ea9 100644
--- a/src/cli/run/integration.test.ts
+++ b/src/cli/run/integration.test.ts
@@ -1,10 +1,13 @@
-import { describe, it, expect, mock, spyOn, beforeEach, afterEach } from "bun:test"
+import { describe, it, expect, mock, spyOn, beforeEach, afterEach, afterAll } from "bun:test"
 import type { RunResult } from "./types"
 import { createJsonOutputManager } from "./json-output"
 import { resolveSession } from "./session-resolver"
 import { executeOnCompleteHook } from "./on-complete-hook"
 import type { OpencodeClient } from "./types"
 
+const realSdk = await import("@opencode-ai/sdk")
+const realPortUtils = await import("../../shared/port-utils")
+
 const mockServerClose = mock(() => {})
 const mockCreateOpencode = mock(() =>
   Promise.resolve({
@@ -17,16 +20,23 @@ const mockIsPortAvailable = mock(() => Promise.resolve(true))
 const mockGetAvailableServerPort = mock(() => Promise.resolve({ port: 9999, wasAutoSelected: false }))
 
 mock.module("@opencode-ai/sdk", () => ({
+  ...realSdk,
   createOpencode: mockCreateOpencode,
   createOpencodeClient: mockCreateOpencodeClient,
 }))
 
 mock.module("../../shared/port-utils", () => ({
+  ...realPortUtils,
   isPortAvailable: mockIsPortAvailable,
   getAvailableServerPort: mockGetAvailableServerPort,
   DEFAULT_SERVER_PORT: 4096,
 }))
 
+afterAll(() => {
+  mock.module("@opencode-ai/sdk", () => ({ ...realSdk }))
+  mock.module("../../shared/port-utils", () => ({ ...realPortUtils }))
+})
+
 const { createServerConnection } = await import("./server-connection")
 
 interface MockWriteStream {
diff --git a/src/cli/run/server-connection.test.ts b/src/cli/run/server-connection.test.ts
index 100154a0e..f9cabc870 100644
--- a/src/cli/run/server-connection.test.ts
+++ b/src/cli/run/server-connection.test.ts
@@ -1,4 +1,7 @@
-import { describe, it, expect, mock, beforeEach, afterEach } from "bun:test"
+import { describe, it, expect, mock, beforeEach, afterEach, afterAll } from "bun:test"
+
+const realSdk = await import("@opencode-ai/sdk")
+const realPortUtils = await import("../../shared/port-utils")
 
 const originalConsole = globalThis.console
 
@@ -15,16 +18,23 @@ const mockGetAvailableServerPort = mock(() => Promise.resolve({ port: 4096, wasA
 const mockConsoleLog = mock(() => {})
 
 mock.module("@opencode-ai/sdk", () => ({
+  ...realSdk,
   createOpencode: mockCreateOpencode,
   createOpencodeClient: mockCreateOpencodeClient,
 }))
 
 mock.module("../../shared/port-utils", () => ({
+  ...realPortUtils,
   isPortAvailable: mockIsPortAvailable,
   getAvailableServerPort: mockGetAvailableServerPort,
   DEFAULT_SERVER_PORT: 4096,
 }))
 
+afterAll(() => {
+  mock.module("@opencode-ai/sdk", () => ({ ...realSdk }))
+  mock.module("../../shared/port-utils", () => ({ ...realPortUtils }))
+})
+
 const { createServerConnection } = await import("./server-connection")
 
 describe("createServerConnection", () => {
diff --git a/src/features/claude-code-mcp-loader/loader.test.ts b/src/features/claude-code-mcp-loader/loader.test.ts
index 848c7aed5..711a721c3 100644
--- a/src/features/claude-code-mcp-loader/loader.test.ts
+++ b/src/features/claude-code-mcp-loader/loader.test.ts
@@ -6,15 +6,20 @@ import { tmpdir } from "os"
 const TEST_DIR = join(tmpdir(), "mcp-loader-test-" + Date.now())
 const TEST_HOME = join(TEST_DIR, "home")
 
+const realOs = await import("os")
+const realShared = await import("../../shared")
+
 describe("getSystemMcpServerNames", () => {
   beforeEach(() => {
     mkdirSync(TEST_DIR, { recursive: true })
     mkdirSync(TEST_HOME, { recursive: true })
     mock.module("os", () => ({
+      ...realOs,
       homedir: () => TEST_HOME,
       tmpdir,
     }))
     mock.module("../../shared", () => ({
+      ...realShared,
       getClaudeConfigDir: () => join(TEST_HOME, ".claude"),
     }))
   })
@@ -22,6 +27,9 @@ describe("getSystemMcpServerNames", () => {
   afterEach(() => {
     mock.restore()
     rmSync(TEST_DIR, { recursive: true, force: true })
+
+    mock.module("os", () => ({ ...realOs }))
+    mock.module("../../shared", () => ({ ...realShared }))
   })
 
   it("returns empty set when no .mcp.json files exist", async () => {
diff --git a/src/features/skill-mcp-manager/manager.test.ts b/src/features/skill-mcp-manager/manager.test.ts
index f65aa5c55..8e5d015a7 100644
--- a/src/features/skill-mcp-manager/manager.test.ts
+++ b/src/features/skill-mcp-manager/manager.test.ts
@@ -1,8 +1,13 @@
-import { describe, it, expect, beforeEach, afterEach, mock, spyOn } from "bun:test"
+import { describe, it, expect, beforeEach, afterEach, mock, spyOn, afterAll } from "bun:test"
 import { SkillMcpManager } from "./manager"
 import type { SkillMcpClientInfo, SkillMcpServerContext } from "./types"
 import type { ClaudeCodeMcpServer } from "../claude-code-mcp-loader/types"
 
+const realStreamableHttp = await import(
+  "@modelcontextprotocol/sdk/client/streamableHttp.js"
+)
+const realMcpOauthProvider = await import("../mcp-oauth/provider")
+
 // Mock the MCP SDK transports to avoid network calls
 const mockHttpConnect = mock(() => Promise.reject(new Error("Mocked HTTP connection failure")))
 const mockHttpClose = mock(() => Promise.resolve())
@@ -37,6 +42,13 @@ mock.module("../mcp-oauth/provider", () => ({
   },
 }))
 
+afterAll(() => {
+  mock.module("@modelcontextprotocol/sdk/client/streamableHttp.js", () => ({
+    ...realStreamableHttp,
+  }))
+  mock.module("../mcp-oauth/provider", () => ({ ...realMcpOauthProvider }))
+})
+
 
 
 
diff --git a/src/features/tmux-subagent/manager.test.ts b/src/features/tmux-subagent/manager.test.ts
index 954a9d8b2..1ab57cbcc 100644
--- a/src/features/tmux-subagent/manager.test.ts
+++ b/src/features/tmux-subagent/manager.test.ts
@@ -1,9 +1,13 @@
-import { describe, test, expect, mock, beforeEach } from 'bun:test'
+import { describe, test, expect, mock, beforeEach, afterAll } from 'bun:test'
 import type { TmuxConfig } from '../../config/schema'
 import type { WindowState, PaneAction } from './types'
 import type { ActionResult, ExecuteContext } from './action-executor'
 import type { TmuxUtilDeps } from './manager'
 
+const realPaneStateQuerier = await import('./pane-state-querier')
+const realActionExecutor = await import('./action-executor')
+const realSharedTmux = await import('../../shared/tmux')
+
 type ExecuteActionsResult = {
   success: boolean
   spawnedPaneId?: string
@@ -71,6 +75,12 @@ mock.module('../../shared/tmux', () => {
   }
 })
 
+afterAll(() => {
+  mock.module('./pane-state-querier', () => ({ ...realPaneStateQuerier }))
+  mock.module('./action-executor', () => ({ ...realActionExecutor }))
+  mock.module('../../shared/tmux', () => ({ ...realSharedTmux }))
+})
+
 const trackedSessions = new Set<string>()
 
 function createMockContext(overrides?: {
diff --git a/src/hooks/anthropic-context-window-limit-recovery/storage.test.ts b/src/hooks/anthropic-context-window-limit-recovery/storage.test.ts
index d5797590f..301af8cb4 100644
--- a/src/hooks/anthropic-context-window-limit-recovery/storage.test.ts
+++ b/src/hooks/anthropic-context-window-limit-recovery/storage.test.ts
@@ -1,4 +1,4 @@
-import { describe, test, expect, mock, beforeEach } from "bun:test"
+import { describe, test, expect, mock, beforeEach, afterAll } from "bun:test"
 import { truncateUntilTargetTokens } from "./storage"
 import * as storage from "./storage"
 
@@ -11,6 +11,10 @@ mock.module("./storage", () => {
   }
 })
 
+afterAll(() => {
+  mock.module("./storage", () => ({ ...storage }))
+})
+
 describe("truncateUntilTargetTokens", () => {
   const sessionID = "test-session"
   
diff --git a/src/hooks/auto-update-checker/hook/background-update-check.test.ts b/src/hooks/auto-update-checker/hook/background-update-check.test.ts
index 8d3009b5d..3f073b1fd 100644
--- a/src/hooks/auto-update-checker/hook/background-update-check.test.ts
+++ b/src/hooks/auto-update-checker/hook/background-update-check.test.ts
@@ -1,4 +1,11 @@
-import { describe, it, expect, mock, beforeEach } from "bun:test"
+import { describe, it, expect, mock, beforeEach, afterAll } from "bun:test"
+
+const realChecker = await import("../checker")
+const realVersionChannel = await import("../version-channel")
+const realCache = await import("../cache")
+const realConfigManager = await import("../../../cli/config-manager")
+const realUpdateToasts = await import("./update-toasts")
+const realLogger = await import("../../../shared/logger")
 
 // Mock modules before importing
 const mockFindPluginEntry = mock(() => null as any)
@@ -39,6 +46,15 @@ mock.module("../../../shared/logger", () => ({
   log: () => {},
 }))
 
+afterAll(() => {
+  mock.module("../checker", () => ({ ...realChecker }))
+  mock.module("../version-channel", () => ({ ...realVersionChannel }))
+  mock.module("../cache", () => ({ ...realCache }))
+  mock.module("../../../cli/config-manager", () => ({ ...realConfigManager }))
+  mock.module("./update-toasts", () => ({ ...realUpdateToasts }))
+  mock.module("../../../shared/logger", () => ({ ...realLogger }))
+})
+
 const { runBackgroundUpdateCheck } = await import("./background-update-check")
 
 describe("runBackgroundUpdateCheck", () => {
diff --git a/src/hooks/claude-code-hooks/stop.test.ts b/src/hooks/claude-code-hooks/stop.test.ts
index 431b90eb4..9834be85e 100644
--- a/src/hooks/claude-code-hooks/stop.test.ts
+++ b/src/hooks/claude-code-hooks/stop.test.ts
@@ -1,7 +1,10 @@
-import { describe, it, expect, mock, beforeEach } from "bun:test"
+import { describe, it, expect, mock, beforeEach, afterAll } from "bun:test"
 import type { ClaudeHooksConfig } from "./types"
 import type { StopContext } from "./stop"
 
+const realCommandExecutor = await import("../../shared/command-executor")
+const realLogger = await import("../../shared/logger")
+
 const mockExecuteHookCommand = mock(() =>
   Promise.resolve({ exitCode: 0, stdout: "", stderr: "" })
 )
@@ -17,6 +20,11 @@ mock.module("../../shared/logger", () => ({
   getLogFilePath: () => "/tmp/test.log",
 }))
 
+afterAll(() => {
+  mock.module("../../shared/command-executor", () => ({ ...realCommandExecutor }))
+  mock.module("../../shared/logger", () => ({ ...realLogger }))
+})
+
 const { executeStopHooks } = await import("./stop")
 
 function createStopContext(overrides?: Partial<StopContext>): StopContext {
diff --git a/src/hooks/comment-checker/cli.test.ts b/src/hooks/comment-checker/cli.test.ts
index 4c7b3bef2..1c75d672c 100644
--- a/src/hooks/comment-checker/cli.test.ts
+++ b/src/hooks/comment-checker/cli.test.ts
@@ -1,10 +1,19 @@
-import { describe, test, expect, mock } from "bun:test"
+import { describe, test, expect, mock, afterAll } from "bun:test"
 import { chmodSync, mkdtempSync, writeFileSync } from "node:fs"
 import { join } from "node:path"
 import { tmpdir } from "node:os"
 
 import type { PendingCall } from "./types"
 
+const realCli = await import("./cli")
+const cliTsHref = new URL("./cli.ts", import.meta.url).href
+
+afterAll(() => {
+  mock.module("./cli", () => ({ ...realCli }))
+  mock.module("./cli.ts", () => ({ ...realCli }))
+  mock.module(cliTsHref, () => ({ ...realCli }))
+})
+
 function createMockInput() {
   return {
     session_id: "test",
diff --git a/src/hooks/comment-checker/hook.apply-patch.test.ts b/src/hooks/comment-checker/hook.apply-patch.test.ts
index ec1b4cd8b..46f3171c9 100644
--- a/src/hooks/comment-checker/hook.apply-patch.test.ts
+++ b/src/hooks/comment-checker/hook.apply-patch.test.ts
@@ -1,4 +1,6 @@
-import { describe, it, expect, mock, beforeEach } from "bun:test"
+import { describe, it, expect, mock, beforeEach, afterAll } from "bun:test"
+
+const realCliRunner = await import("./cli-runner")
 
 const processApplyPatchEditsWithCli = mock(async () => {})
 
@@ -10,6 +12,10 @@ mock.module("./cli-runner", () => ({
   processApplyPatchEditsWithCli,
 }))
 
+afterAll(() => {
+  mock.module("./cli-runner", () => ({ ...realCliRunner }))
+})
+
 const { createCommentCheckerHooks } = await import("./hook")
 
 describe("comment-checker apply_patch integration", () => {
diff --git a/src/hooks/compaction-context-injector/index.test.ts b/src/hooks/compaction-context-injector/index.test.ts
index a2813916f..737a4e5bb 100644
--- a/src/hooks/compaction-context-injector/index.test.ts
+++ b/src/hooks/compaction-context-injector/index.test.ts
@@ -1,4 +1,6 @@
-import { describe, expect, it, mock } from "bun:test"
+import { describe, expect, it, mock, afterAll } from "bun:test"
+
+const realSystemDirective = await import("../../shared/system-directive")
 
 mock.module("../../shared/system-directive", () => ({
   createSystemDirective: (type: string) => `[DIRECTIVE:${type}]`,
@@ -14,6 +16,10 @@ mock.module("../../shared/system-directive", () => ({
   },
 }))
 
+afterAll(() => {
+  mock.module("../../shared/system-directive", () => ({ ...realSystemDirective }))
+})
+
 import { createCompactionContextInjector } from "./index"
 import { TaskHistory } from "../../features/background-agent/task-history"
 
diff --git a/src/hooks/rules-injector/injector.test.ts b/src/hooks/rules-injector/injector.test.ts
index e07b7fc42..36b815f1e 100644
--- a/src/hooks/rules-injector/injector.test.ts
+++ b/src/hooks/rules-injector/injector.test.ts
@@ -1,4 +1,4 @@
-import { afterEach, beforeEach, describe, expect, it, mock } from "bun:test";
+import { afterEach, beforeEach, describe, expect, it, mock, afterAll } from "bun:test";
 import * as fs from "node:fs";
 import { mkdirSync, rmSync, writeFileSync } from "node:fs";
 import * as os from "node:os";
@@ -6,6 +6,10 @@ import { tmpdir } from "node:os";
 import { join } from "node:path";
 import { RULES_INJECTOR_STORAGE } from "./constants";
 
+const realNodeFs = await import("node:fs");
+const realNodeOs = await import("node:os");
+const realMatcher = await import("./matcher");
+
 type StatSnapshot = { mtimeMs: number; size: number };
 
 let trackedRulePath = "";
@@ -56,6 +60,12 @@ mock.module("./matcher", () => ({
   isDuplicateByContentHash: (hash: string, cache: Set<string>) => cache.has(hash),
 }));
 
+afterAll(() => {
+  mock.module("node:fs", () => ({ ...realNodeFs }));
+  mock.module("node:os", () => ({ ...realNodeOs }));
+  mock.module("./matcher", () => ({ ...realMatcher }));
+});
+
 function createOutput(): { title: string; output: string; metadata: unknown } {
   return { title: "tool", output: "", metadata: {} };
 }
diff --git a/src/tools/lsp/client.test.ts b/src/tools/lsp/client.test.ts
index 8c805d144..c750f3dea 100644
--- a/src/tools/lsp/client.test.ts
+++ b/src/tools/lsp/client.test.ts
@@ -2,7 +2,9 @@ import { mkdtempSync, rmSync, writeFileSync } from "node:fs"
 import { join } from "node:path"
 import { tmpdir } from "node:os"
 
-import { describe, it, expect, spyOn, mock, beforeEach, afterEach } from "bun:test"
+import { describe, it, expect, spyOn, mock, beforeEach, afterEach, afterAll } from "bun:test"
+
+const realJsonRpcNode = await import("vscode-jsonrpc/node")
 
 mock.module("vscode-jsonrpc/node", () => ({
   createMessageConnection: () => {
@@ -12,6 +14,10 @@ mock.module("vscode-jsonrpc/node", () => ({
   StreamMessageWriter: function StreamMessageWriter() {},
 }))
 
+afterAll(() => {
+  mock.module("vscode-jsonrpc/node", () => ({ ...realJsonRpcNode }))
+})
+
 import { LSPClient, lspManager, validateCwd } from "./client"
 import type { ResolvedServer } from "./types"
 
diff --git a/src/tools/session-manager/storage.test.ts b/src/tools/session-manager/storage.test.ts
index 76507867a..1f7a400c3 100644
--- a/src/tools/session-manager/storage.test.ts
+++ b/src/tools/session-manager/storage.test.ts
@@ -1,9 +1,11 @@
-import { describe, test, expect, beforeEach, afterEach, mock } from "bun:test"
+import { describe, test, expect, beforeEach, afterEach, afterAll, mock } from "bun:test"
 import { mkdirSync, writeFileSync, rmSync, existsSync } from "node:fs"
 import { join } from "node:path"
 import { tmpdir } from "node:os"
 import { randomUUID } from "node:crypto"
 
+const realConstants = await import("./constants")
+
 const TEST_DIR = join(tmpdir(), `omo-test-session-manager-${randomUUID()}`)
 const TEST_MESSAGE_STORAGE = join(TEST_DIR, "message")
 const TEST_PART_STORAGE = join(TEST_DIR, "part")
@@ -26,6 +28,10 @@ mock.module("./constants", () => ({
   TOOL_NAME_PREFIX: "session_",
 }))
 
+afterAll(() => {
+  mock.module("./constants", () => ({ ...realConstants }))
+})
+
 const { getAllSessions, getMessageDir, sessionExists, readSessionMessages, readSessionTodos, getSessionInfo } =
   await import("./storage")
 
diff --git a/src/tools/skill/tools.test.ts b/src/tools/skill/tools.test.ts
index e5ce213e9..a4b5bb479 100644
--- a/src/tools/skill/tools.test.ts
+++ b/src/tools/skill/tools.test.ts
@@ -1,4 +1,4 @@
-import { describe, it, expect, beforeEach, mock, spyOn } from "bun:test"
+import { describe, it, expect, beforeEach, mock, spyOn, afterAll } from "bun:test"
 import type { ToolContext } from "@opencode-ai/plugin/tool"
 import * as fs from "node:fs"
 import { createSkillTool } from "./tools"
@@ -8,6 +8,8 @@ import type { Tool as McpTool } from "@modelcontextprotocol/sdk/types.js"
 
 const originalReadFileSync = fs.readFileSync.bind(fs)
 
+const realNodeFs = await import("node:fs")
+
 mock.module("node:fs", () => ({
   ...fs,
   readFileSync: (path: string, encoding?: string) => {
@@ -21,6 +23,10 @@ Test skill body content`
   },
 }))
 
+afterAll(() => {
+  mock.module("node:fs", () => ({ ...realNodeFs }))
+})
+
 function createMockSkill(name: string, options: { agent?: string } = {}): LoadedSkill {
   return {
     name,