diff --git a/apps/server/src/orchestration-v2/Adapters/CodexAdapterV2.test.ts b/apps/server/src/orchestration-v2/Adapters/CodexAdapterV2.test.ts
index 54a4c2e2bf28e..1734f9e0af88b 100644
--- a/apps/server/src/orchestration-v2/Adapters/CodexAdapterV2.test.ts
+++ b/apps/server/src/orchestration-v2/Adapters/CodexAdapterV2.test.ts
@@ -1530,6 +1530,14 @@ describe("CodexAdapterV2 post-settle continuation", () => {
               url: "http://127.0.0.1:43123/mcp",
               tool_timeout_sec: 3_900,
               http_headers: { Authorization: "Bearer secret-codex-token" },
+              disabled_tools: ["t3_thread_wait"],
+            },
+            "mcp_servers.t3code": {
+              url: "http://127.0.0.1:43123/mcp",
+              tool_timeout_sec: 3_900,
+              http_headers: { Authorization: "Bearer secret-codex-token" },
+              enabled_tools: ["t3_thread_wait"],
+              omit_tools_from: ["code_mode", "deferred"],
             },
           },
         },
diff --git a/apps/server/src/orchestration-v2/Adapters/CodexAdapterV2.ts b/apps/server/src/orchestration-v2/Adapters/CodexAdapterV2.ts
index fa6bb58a9dcbe..bda631ec99c66 100644
--- a/apps/server/src/orchestration-v2/Adapters/CodexAdapterV2.ts
+++ b/apps/server/src/orchestration-v2/Adapters/CodexAdapterV2.ts
@@ -1334,6 +1334,9 @@ export const CODEX_THREAD_CONFIG = {
 
 // T3 waits can block for an hour; keep Codex's MCP timeout above that.
 const CODEX_T3_MCP_TOOL_TIMEOUT_SEC = 65 * 60;
+// Calls arrive as `t3code.<tool>`; t3McpToolPresentation.ts must keep resolving that form.
+const CODEX_T3_WAIT_MCP_SERVER = "t3code";
+const CODEX_DIRECT_ONLY_T3_TOOL = "t3_thread_wait";
 
 function codexThreadRuntimeParams(input: {
   readonly threadId: ThreadId | null;
@@ -1346,6 +1349,14 @@ function codexThreadRuntimeParams(input: {
   readonly config: Readonly<Record<string, Schema.Json>>;
 } {
   const { mcpSession } = input;
+  const t3Server =
+    mcpSession === undefined
+      ? undefined
+      : {
+          url: mcpSession.endpoint,
+          tool_timeout_sec: CODEX_T3_MCP_TOOL_TIMEOUT_SEC,
+          http_headers: { Authorization: mcpSession.authorizationHeader },
+        };
   return {
     ...(input.runtimePolicy?.cwd == null ? {} : { cwd: input.runtimePolicy.cwd }),
     ...(input.modelSelection === undefined ? {} : { model: input.modelSelection.model }),
@@ -1355,16 +1366,17 @@ function codexThreadRuntimeParams(input: {
       ...(input.threadId === null
         ? {}
         : { [`shell_environment_policy.set.${PortScanner.AGENT_THREAD_ENV}`]: input.threadId }),
-      ...(mcpSession === undefined
+      ...(t3Server === undefined
         ? {}
         : {
-            // Override only T3's server so launch-argument MCP servers survive.
-            "mcp_servers.t3-code": {
-              url: mcpSession.endpoint,
-              tool_timeout_sec: CODEX_T3_MCP_TOOL_TIMEOUT_SEC,
-              http_headers: {
-                Authorization: mcpSession.authorizationHeader,
-              },
+            // Override only T3's servers so launch-argument MCP servers survive.
+            "mcp_servers.t3-code": { ...t3Server, disabled_tools: [CODEX_DIRECT_ONLY_T3_TOOL] },
+            // Code Mode runs a blocking wait as a nested call, and the model keeps working
+            // around it. A second, direct-only registration makes it a plain tool call.
+            [`mcp_servers.${CODEX_T3_WAIT_MCP_SERVER}`]: {
+              ...t3Server,
+              enabled_tools: [CODEX_DIRECT_ONLY_T3_TOOL],
+              omit_tools_from: ["code_mode", "deferred"],
             },
           }),
     },
diff --git a/docs/orchestration-v2/orchestrator-mcp-server.md b/docs/orchestration-v2/orchestrator-mcp-server.md
index f46803f9d67b6..77f95873f06a6 100644
--- a/docs/orchestration-v2/orchestrator-mcp-server.md
+++ b/docs/orchestration-v2/orchestrator-mcp-server.md
@@ -58,17 +58,18 @@ check the `orchestration` capability before reading or mutating state.
 
 ### Codex V2
 
-Codex app-server receives the remote MCP server through command-line config
-overrides:
-
-```text
--c mcp_servers.t3-code.url=http://127.0.0.1:<port>/mcp
--c mcp_servers.t3-code.bearer_token_env_var="T3_MCP_BEARER_TOKEN"
-```
-
-The provider-session token is placed in `T3_MCP_BEARER_TOKEN`. Both the
-production Codex launcher and the injectable test launcher use the same
-projection helper.
+Codex gets T3's MCP server in each thread's `thread/start`, `thread/resume`,
+and `thread/fork` config, with the provider-session token in an
+`Authorization` header. The same server is registered twice:
+
+- `t3-code`: every tool except `t3_thread_wait`.
+- `t3code`: only `t3_thread_wait`, with `omit_tools_from = ["code_mode", "deferred"]`.
+
+Code Mode runs a nested call as part of a script, so the model keeps working
+while a blocking wait runs. The second entry makes the wait a direct tool call,
+like Codex's own wait tools. Codex reports calls as `<server>.<tool>`, so
+`packages/shared/src/t3McpToolPresentation.ts` must resolve both server names.
+Tool display and pending-work detection depend on it.
 
 ### Claude Agent SDK V2
 
diff --git a/packages/shared/src/t3McpToolPresentation.test.ts b/packages/shared/src/t3McpToolPresentation.test.ts
index 1c2683753656c..cd27e5cc452bd 100644
--- a/packages/shared/src/t3McpToolPresentation.test.ts
+++ b/packages/shared/src/t3McpToolPresentation.test.ts
@@ -16,6 +16,7 @@ describe("resolveT3McpToolPresentation", () => {
         "mcp__t3_code__",
         "mcp__t3code__",
         "T3-code.",
+        "t3code.",
         "t3_code/",
         "t3code:",
         "mcp_t3-code_",