diff --git a/src/agents/pi-embedded-runner/run.overflow-compaction.e2e.test.ts b/src/agents/pi-embedded-runner/run.overflow-compaction.e2e.test.ts
index d9ce20b07e9..20097404db5 100644
--- a/src/agents/pi-embedded-runner/run.overflow-compaction.e2e.test.ts
+++ b/src/agents/pi-embedded-runner/run.overflow-compaction.e2e.test.ts
@@ -354,6 +354,22 @@ describe("overflow compaction in run loop", () => {
     expect(log.warn).not.toHaveBeenCalledWith(expect.stringContaining("source=assistantError"));
   });
 
+  it("returns an explicit timeout payload when the run times out before producing any reply", async () => {
+    mockedRunEmbeddedAttempt.mockResolvedValue(
+      makeAttemptResult({
+        aborted: true,
+        timedOut: true,
+        timedOutDuringCompaction: false,
+        assistantTexts: [],
+      }),
+    );
+
+    const result = await runEmbeddedPiAgent(baseParams);
+
+    expect(result.payloads?.[0]?.isError).toBe(true);
+    expect(result.payloads?.[0]?.text).toContain("timed out");
+  });
+
   it("sets promptTokens from the latest model call usage, not accumulated attempt usage", async () => {
     mockedRunEmbeddedAttempt.mockResolvedValue(
       makeAttemptResult({
diff --git a/src/agents/pi-embedded-runner/run.ts b/src/agents/pi-embedded-runner/run.ts
index 74a07e37f09..666431ffa7e 100644
--- a/src/agents/pi-embedded-runner/run.ts
+++ b/src/agents/pi-embedded-runner/run.ts
@@ -907,6 +907,31 @@ export async function runEmbeddedPiAgent(
             inlineToolResultsAllowed: false,
           });
 
+          // Timeout aborts can leave the run without any assistant payloads.
+          // Emit an explicit timeout error instead of silently completing, so
+          // callers do not lose the turn as an orphaned user message.
+          if (timedOut && !timedOutDuringCompaction && payloads.length === 0) {
+            return {
+              payloads: [
+                {
+                  text:
+                    "Request timed out before a response was generated. " +
+                    "Please try again, or increase `agents.defaults.timeoutSeconds` in your config.",
+                  isError: true,
+                },
+              ],
+              meta: {
+                durationMs: Date.now() - started,
+                agentMeta,
+                aborted,
+                systemPromptReport: attempt.systemPromptReport,
+              },
+              didSendViaMessagingTool: attempt.didSendViaMessagingTool,
+              messagingToolSentTexts: attempt.messagingToolSentTexts,
+              messagingToolSentTargets: attempt.messagingToolSentTargets,
+            };
+          }
+
           log.debug(
             `embedded run done: runId=${params.runId} sessionId=${params.sessionId} durationMs=${Date.now() - started} aborted=${aborted}`,
           );