diff --git a/packages/coding-agent/src/extensibility/extensions/runner.ts b/packages/coding-agent/src/extensibility/extensions/runner.ts
index 50289f977..f4f765f10 100644
--- a/packages/coding-agent/src/extensibility/extensions/runner.ts
+++ b/packages/coding-agent/src/extensibility/extensions/runner.ts
@@ -1053,13 +1053,6 @@ export class ExtensionRunner {
 					} catch (error) {
 						handlerFailure ??= { error };
 					}
-					const registrationBarrier = this.#toolRegistrationBarrier;
-					if (registrationBarrier) {
-						// Also wait for detached registrations that were scheduled before this
-						// handler completed. Their failures are reported at registration time,
-						// not attributed to this unrelated handler.
-						await registrationBarrier;
-					}
 					return result;
 				},
 				timeoutMs,
diff --git a/packages/coding-agent/src/session/session-tools.ts b/packages/coding-agent/src/session/session-tools.ts
index 10f9eb9e5..9caa6052a 100644
--- a/packages/coding-agent/src/session/session-tools.ts
+++ b/packages/coding-agent/src/session/session-tools.ts
@@ -386,7 +386,7 @@ export class SessionTools {
 			return this.#toolRegistryMutationScope.run(true, mutation);
 		});
 		const operation = untilAborted(signal, serialized);
-		this.#toolRegistryMutationTail = operation.then(
+		this.#toolRegistryMutationTail = serialized.then(
 			() => undefined,
 			() => undefined,
 		);
diff --git a/packages/coding-agent/test/agent-session-tool-rebuild-skip.test.ts b/packages/coding-agent/test/agent-session-tool-rebuild-skip.test.ts
index 1276b504b..fb4f4d93f 100644
--- a/packages/coding-agent/test/agent-session-tool-rebuild-skip.test.ts
+++ b/packages/coding-agent/test/agent-session-tool-rebuild-skip.test.ts
@@ -294,6 +294,37 @@ describe("AgentSession refreshMCPTools rebuild skipping", () => {
 		expect(session.systemPrompt).toEqual(["tools:read,mcp__nucleus_search,late_prompt_tool"]);
 	});
 
+	it("keeps queued mutations serialized when a waiting caller aborts", async () => {
+		const firstMutationEntered = Promise.withResolvers<void>();
+		const releaseFirstMutation = Promise.withResolvers<void>();
+		const { session } = newSession(async toolNames => `tools:${toolNames.join(",")}`);
+		const firstMutation = session.runToolRegistryMutation(async () => {
+			firstMutationEntered.resolve();
+			await releaseFirstMutation.promise;
+		});
+		await firstMutationEntered.promise;
+
+		const controller = new AbortController();
+		let abortedMutationRan = false;
+		const abortedMutation = session.runToolRegistryMutation(async () => {
+			abortedMutationRan = true;
+		}, controller.signal);
+		controller.abort(new Error("cancel queued mutation"));
+		await expect(abortedMutation).rejects.toThrow("cancel queued mutation");
+
+		let thirdMutationRan = false;
+		const thirdMutation = session.runToolRegistryMutation(async () => {
+			thirdMutationRan = true;
+		});
+		await Promise.resolve();
+		expect(thirdMutationRan).toBe(false);
+
+		releaseFirstMutation.resolve();
+		await Promise.all([firstMutation, thirdMutation]);
+		expect(abortedMutationRan).toBe(false);
+		expect(thirdMutationRan).toBe(true);
+	});
+
 	it("drops queued and in-flight MCP prompt commits when disposal begins", async () => {
 		const firstRebuildStarted = Promise.withResolvers<void>();
 		const releaseFirstRebuild = Promise.withResolvers<void>();
diff --git a/packages/coding-agent/test/extensions-runner.test.ts b/packages/coding-agent/test/extensions-runner.test.ts
index d65a3b69a..e6d69ae76 100644
--- a/packages/coding-agent/test/extensions-runner.test.ts
+++ b/packages/coding-agent/test/extensions-runner.test.ts
@@ -1448,6 +1448,56 @@ describe("ExtensionRunner", () => {
 			});
 		});
 
+		it("does not charge detached registrations to unrelated tool-call handlers", async () => {
+			const extensionPath = path.join(tempDir.path(), "detached-registration-barrier.ts");
+			fs.writeFileSync(
+				extensionPath,
+				`
+					export default function(pi) {
+						const { Type } = pi.typebox;
+						pi.registerTool({
+							name: "detached_source_tool",
+							label: "Detached Source Tool",
+							description: "Provides a registration event for the detached barrier test.",
+							parameters: Type.Object({}),
+							execute: async () => ({ content: [{ type: "text", text: "ok" }], details: {} }),
+						});
+						pi.on("tool_call", () => undefined);
+					}
+				`,
+			);
+
+			const loaded = await loadTestExtensions([extensionPath]);
+			const runner = new ExtensionRunner(
+				loaded.extensions,
+				loaded.runtime,
+				tempDir.path(),
+				sessionManager,
+				modelRegistry,
+			);
+			runner.onToolRegistered(() => Promise.withResolvers<void>().promise);
+			const extension = loaded.extensions[0];
+			const registrationListener = extension?.toolRegistrationListeners?.values().next().value;
+			if (!registrationListener) throw new Error("expected registration listener");
+			registrationListener("detached_source_tool");
+
+			const errors: ExtensionError[] = [];
+			runner.onError(error => {
+				errors.push(error);
+			});
+			testSetExtensionHandlerTimeoutMs(10);
+
+			const result = await runner.emitToolCall({
+				type: "tool_call",
+				toolName: "unrelated",
+				toolCallId: "unrelated-call",
+				input: {},
+			});
+
+			expect(result).toBeUndefined();
+			expect(errors).toEqual([]);
+		});
+
 		it("aborts a tool_call handler's confirmation before returning its timeout block", async () => {
 			const extensionPath = path.join(tempDir.path(), "confirm-tool-call.ts");
 			const markerPath = path.join(tempDir.path(), "confirm-settled.txt");
diff --git a/packages/coding-agent/test/sdk-tool-activation.test.ts b/packages/coding-agent/test/sdk-tool-activation.test.ts
index 5c036e944..9b5ed958d 100644
--- a/packages/coding-agent/test/sdk-tool-activation.test.ts
+++ b/packages/coding-agent/test/sdk-tool-activation.test.ts
@@ -178,6 +178,7 @@ describe("createAgentSession defaultInactive tool activation", () => {
 			});
 			pi.on("input", async () => {
 				await startupPromise;
+				await pi.setActiveTools([...pi.getActiveTools(), "late_active_tool"]);
 			});
 		};
 
@@ -190,10 +191,19 @@ describe("createAgentSession defaultInactive tool activation", () => {
 			expect(session.getAllToolNames()).not.toContain("late_active_tool");
 			const runner = session.extensionRunner;
 			if (!runner) throw new Error("expected extension runner");
-			await runner.emit({ type: "session_start" });
+			const errors: string[] = [];
+			const unsubscribe = runner.onError(error => {
+				errors.push(error.error);
+			});
+			await initializeExtensions(session, {
+				reportSendError: vi.fn(),
+				reportRuntimeError: vi.fn(),
+			});
 			expect(session.getAllToolNames()).not.toContain("late_active_tool");
 			startupGate.resolve();
 			await runner.emitInput("probe", undefined, "interactive");
+			unsubscribe();
+			expect(errors).toEqual([]);
 
 			expect(session.getAllToolNames()).toEqual(expect.arrayContaining(["late_active_tool", "late_inactive_tool"]));
 			expect(session.getEnabledToolNames()).toContain("late_active_tool");