diff --git a/scripts/e2e/cron-mcp-cleanup-docker-client.ts b/scripts/e2e/cron-mcp-cleanup-docker-client.ts
index 567fb347381..4806afdf16b 100644
--- a/scripts/e2e/cron-mcp-cleanup-docker-client.ts
+++ b/scripts/e2e/cron-mcp-cleanup-docker-client.ts
@@ -205,17 +205,21 @@ async function runSubagentCleanupScenario(params: {
   const { gateway, pidPath, pidsPath, exitPath } = params;
   await resetProbeFiles({ pidPath, pidsPath, exitPath });
 
-  const run = await gateway.request<AgentRunResult>("agent", {
-    message: "Use available context and then stop.",
-    sessionKey: `agent:main:subagent:docker-${randomUUID()}`,
-    agentId: "main",
-    lane: "subagent",
-    cleanupBundleMcpOnRunEnd: true,
-    idempotencyKey: randomUUID(),
-    deliver: false,
-    timeout: 90,
-    bestEffortDeliver: true,
-  });
+  const run = await gateway.request<AgentRunResult>(
+    "agent",
+    {
+      message: "Use available context and then stop.",
+      sessionKey: `agent:main:subagent:docker-${randomUUID()}`,
+      agentId: "main",
+      lane: "subagent",
+      cleanupBundleMcpOnRunEnd: true,
+      idempotencyKey: randomUUID(),
+      deliver: false,
+      timeout: 90,
+      bestEffortDeliver: true,
+    },
+    { timeoutMs: 240_000 },
+  );
   assert(
     run.status === "accepted" && run.runId,
     `agent did not accept subagent cleanup run: ${JSON.stringify(run)}`,
diff --git a/scripts/e2e/mcp-channels-harness.ts b/scripts/e2e/mcp-channels-harness.ts
index 3e2d4781145..000552ab701 100644
--- a/scripts/e2e/mcp-channels-harness.ts
+++ b/scripts/e2e/mcp-channels-harness.ts
@@ -33,7 +33,7 @@ export const ClaudePermissionNotificationSchema = z.object({
 export type ClaudeChannelNotification = z.infer<typeof ClaudeChannelNotificationSchema>["params"];
 
 export type GatewayRpcClient = {
-  request<T>(method: string, params?: unknown): Promise<T>;
+  request<T>(method: string, params?: unknown, opts?: { timeoutMs?: number }): Promise<T>;
   events: Array<{ event: string; payload: Record<string, unknown> }>;
   close(): Promise<void>;
 };
@@ -266,8 +266,12 @@ async function connectGatewayOnce(params: {
   await sendGatewayRequest("sessions.subscribe", {}, GATEWAY_RPC_TIMEOUT_MS);
 
   return {
-    request(method, requestParams) {
-      return sendGatewayRequest(method, requestParams, GATEWAY_REQUEST_TIMEOUT_MS);
+    request(method, requestParams, opts) {
+      return sendGatewayRequest(
+        method,
+        requestParams,
+        opts?.timeoutMs ?? GATEWAY_REQUEST_TIMEOUT_MS,
+      );
     },
     events,
     async close() {