diff --git a/packages/core/src/core/geminiChat.test.ts b/packages/core/src/core/geminiChat.test.ts
index 741e369f58..6e3b1544aa 100644
--- a/packages/core/src/core/geminiChat.test.ts
+++ b/packages/core/src/core/geminiChat.test.ts
@@ -12,7 +12,6 @@ import {
   GeminiChat,
   InvalidStreamError,
   StreamEventType,
-  SYNTHETIC_THOUGHT_SIGNATURE,
   type StreamEvent,
 } from './geminiChat.js';
 import type { Config } from '../config/config.js';
@@ -1951,96 +1950,6 @@ describe('GeminiChat', () => {
     });
   });
 
-  describe('ensureActiveLoopHasThoughtSignatures', () => {
-    it('should add thoughtSignature to the first functionCall in each model turn of the active loop', () => {
-      const chat = new GeminiChat(mockConfig, '', [], []);
-      const history: Content[] = [
-        { role: 'user', parts: [{ text: 'Old message' }] },
-        {
-          role: 'model',
-          parts: [{ functionCall: { name: 'old_tool', args: {} } }],
-        },
-        { role: 'user', parts: [{ text: 'Find a restaurant' }] }, // active loop starts here
-        {
-          role: 'model',
-          parts: [
-            { functionCall: { name: 'find_restaurant', args: {} } }, // This one gets a signature
-            { functionCall: { name: 'find_restaurant_2', args: {} } }, // This one does NOT
-          ],
-        },
-        {
-          role: 'user',
-          parts: [
-            { functionResponse: { name: 'find_restaurant', response: {} } },
-          ],
-        },
-        {
-          role: 'model',
-          parts: [
-            {
-              functionCall: { name: 'tool_with_sig', args: {} },
-              thoughtSignature: 'existing-sig',
-            },
-            { functionCall: { name: 'another_tool', args: {} } }, // This one does NOT get a signature
-          ],
-        },
-      ];
-
-      const newContents = chat.ensureActiveLoopHasThoughtSignatures(history);
-
-      // Outside active loop - unchanged
-      expect(newContents[1]?.parts?.[0]).not.toHaveProperty('thoughtSignature');
-
-      // Inside active loop, first model turn
-      // First function call gets a signature
-      expect(newContents[3]?.parts?.[0]?.thoughtSignature).toBe(
-        SYNTHETIC_THOUGHT_SIGNATURE,
-      );
-      // Second function call does NOT
-      expect(newContents[3]?.parts?.[1]).not.toHaveProperty('thoughtSignature');
-
-      // User functionResponse part - unchanged (this is not a model turn)
-      expect(newContents[4]?.parts?.[0]).not.toHaveProperty('thoughtSignature');
-
-      // Inside active loop, second model turn
-      // First function call already has a signature, so nothing changes
-      expect(newContents[5]?.parts?.[0]?.thoughtSignature).toBe('existing-sig');
-      // Second function call does NOT get a signature
-      expect(newContents[5]?.parts?.[1]).not.toHaveProperty('thoughtSignature');
-    });
-
-    it('should not modify contents if there is no user text message', () => {
-      const chat = new GeminiChat(mockConfig, '', [], []);
-      const history: Content[] = [
-        {
-          role: 'user',
-          parts: [{ functionResponse: { name: 'tool1', response: {} } }],
-        },
-        {
-          role: 'model',
-          parts: [{ functionCall: { name: 'tool2', args: {} } }],
-        },
-      ];
-      const newContents = chat.ensureActiveLoopHasThoughtSignatures(history);
-      expect(newContents).toEqual(history);
-      expect(newContents[1]?.parts?.[0]).not.toHaveProperty('thoughtSignature');
-    });
-
-    it('should handle an empty history', () => {
-      const chat = new GeminiChat(mockConfig, '', []);
-      const history: Content[] = [];
-      const newContents = chat.ensureActiveLoopHasThoughtSignatures(history);
-      expect(newContents).toEqual([]);
-    });
-
-    it('should handle history with only a user message', () => {
-      const chat = new GeminiChat(mockConfig, '', []);
-      const history: Content[] = [{ role: 'user', parts: [{ text: 'Hello' }] }];
-      const newContents = chat.ensureActiveLoopHasThoughtSignatures(history);
-      expect(newContents).toEqual(history);
-    });
-  });
-
   describe('Availability Service Integration', () => {
     let mockAvailabilityService: ModelAvailabilityService;
 
diff --git a/packages/core/src/core/geminiChat.ts b/packages/core/src/core/geminiChat.ts
index bd7182fd03..894dd336a5 100644
--- a/packages/core/src/core/geminiChat.ts
+++ b/packages/core/src/core/geminiChat.ts
@@ -32,6 +32,7 @@ import type { CompletedToolCall } from './coreToolScheduler.js';
 import {
   logContentRetry,
   logContentRetryFailure,
+  logOrphanedFunctionCallFixed,
 } from '../telemetry/loggers.js';
 import {
   ChatRecordingService,
@@ -40,6 +41,7 @@ import {
 import {
   ContentRetryEvent,
   ContentRetryFailureEvent,
+  OrphanedFunctionCallFixedEvent,
 } from '../telemetry/types.js';
 import { handleFallback } from '../fallback/handler.js';
 import { isFunctionResponse } from '../utils/messageInspectors.js';
@@ -441,9 +443,6 @@ export class GeminiChat {
     prompt_id: string,
     abortSignal: AbortSignal,
   ): Promise<AsyncGenerator<GenerateContentResponse>> {
-    const contentsForPreviewModel =
-      this.ensureActiveLoopHasThoughtSignatures(requestContents);
-
     // Track final request parameters for AfterModel hooks
     const {
       model: availabilityFinalModel,
@@ -451,6 +450,15 @@ export class GeminiChat {
       maxAttempts: availabilityMaxAttempts,
     } = applyModelSelection(this.config, modelConfigKey);
 
+    // Ensure all function calls in the history have responses.
+    requestContents = this.ensureActiveLoopHasFunctionResponses(
+      requestContents,
+      availabilityFinalModel,
+    );
+
+    const contentsForPreviewModel =
+      this.ensureActiveLoopHasThoughtSignatures(requestContents);
+
     let lastModelToUse = availabilityFinalModel;
     let currentGenerateContentConfig: GenerateContentConfig =
       newAvailabilityConfig;
@@ -698,20 +706,105 @@ export class GeminiChat {
     });
   }
 
+  private findActiveLoopStartIndex(contents: Content[]): number {
+    for (let i = contents.length - 1; i >= 0; i--) {
+      const content = contents[i];
+      if (content.role === 'user' && content.parts?.some((part) => part.text)) {
+        return i;
+      }
+    }
+    return -1;
+  }
+
+  // To ensure our requests validate, every function call in the history
+  // must have a valid function response. If we do not do this, we will get
+  // back 400 errors from the API.
+  ensureActiveLoopHasFunctionResponses(
+    requestContents: Content[],
+    model: string,
+  ): Content[] {
+    // Iterate through every message in the history, ensuring that every
+    // function call in each model message has a corresponding function
+    // response in the next user message.
+    const newContents = requestContents.slice(); // Shallow copy the array
+    for (let i = 0; i < newContents.length; i++) {
+      const content = newContents[i];
+      if (content.role === 'model' && content.parts) {
+        const functionCalls = content.parts.filter((part) => part.functionCall);
+        if (functionCalls.length > 0) {
+          const nextIndex = i + 1;
+          const nextContent =
+            nextIndex < newContents.length ? newContents[nextIndex] : undefined;
+
+          const missingResponses: Part[] = [];
+          for (const callPart of functionCalls) {
+            const call = callPart.functionCall!;
+            const callId = (call as { id: string })['id'];
+
+            // Check if the next turn is a user turn and has a response for this call.
+            const hasResponse =
+              nextContent?.role === 'user' &&
+              nextContent.parts?.some((part) => {
+                if (!part.functionResponse) {
+                  return false;
+                }
+                if (callId && part.functionResponse.id) {
+                  return part.functionResponse.id === callId;
+                }
+                return part.functionResponse.name === call.name;
+              });
+
+            if (!hasResponse) {
+              logOrphanedFunctionCallFixed(
+                this.config,
+                new OrphanedFunctionCallFixedEvent(
+                  model,
+                  call.name ?? 'unknown',
+                ),
+              );
+
+              missingResponses.push({
+                functionResponse: {
+                  name: call.name,
+                  id: callId,
+                  response: {
+                    status: 'unknown',
+                    message:
+                      'The status of this function call is unknown. Please validate the state of the world before continuing.',
+                  },
+                },
+              });
+            }
+          }
+
+          if (missingResponses.length > 0) {
+            if (nextContent?.role === 'user') {
+              // Add missing responses to the existing user turn.
+              const updatedNextContent = {
+                ...nextContent,
+                parts: [...missingResponses, ...(nextContent.parts || [])],
+              };
+              newContents[nextIndex] = updatedNextContent;
+            } else {
+              // Insert a new user turn with the missing responses.
+              const newUserContent: Content = {
+                role: 'user',
+                parts: missingResponses,
+              };
+              newContents.splice(nextIndex, 0, newUserContent);
+            }
+          }
+        }
+      }
+    }
+    return newContents;
+  }
+
   // To ensure our requests validate, the first function call in every model
   // turn within the active loop must have a `thoughtSignature` property.
   // If we do not do this, we will get back 400 errors from the API.
   ensureActiveLoopHasThoughtSignatures(requestContents: Content[]): Content[] {
-    // First, find the start of the active loop by finding the last user turn
-    // with a text message, i.e. that is not a function response.
-    let activeLoopStartIndex = -1;
-    for (let i = requestContents.length - 1; i >= 0; i--) {
-      const content = requestContents[i];
-      if (content.role === 'user' && content.parts?.some((part) => part.text)) {
-        activeLoopStartIndex = i;
-        break;
-      }
-    }
+    const activeLoopStartIndex = this.findActiveLoopStartIndex(requestContents);
 
     if (activeLoopStartIndex === -1) {
       return requestContents;
diff --git a/packages/core/src/core/geminiChat_history_repair.test.ts b/packages/core/src/core/geminiChat_history_repair.test.ts
new file mode 100644
index 0000000000..4f26863bb1
--- /dev/null
+++ b/packages/core/src/core/geminiChat_history_repair.test.ts
@@ -0,0 +1,298 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { describe, it, expect, vi, beforeEach } from 'vitest';
+import type { Content } from '@google/genai';
+import { GeminiChat, SYNTHETIC_THOUGHT_SIGNATURE } from './geminiChat.js';
+import type { Config } from '../config/config.js';
+import { DEFAULT_THINKING_MODE } from '../config/models.js';
+import { createMockMessageBus } from '../test-utils/mock-message-bus.js';
+import { createAvailabilityServiceMock } from '../availability/testUtils.js';
+
+vi.mock('node:fs', () => ({
+  default: {
+    mkdirSync: vi.fn(),
+    writeFileSync: vi.fn(),
+    readFileSync: vi.fn(() => {
+      const error = new Error('ENOENT');
+      (error as NodeJS.ErrnoException).code = 'ENOENT';
+      throw error;
+    }),
+    existsSync: vi.fn(() => false),
+  },
+}));
+
+const { mockLogOrphanedFunctionCallFixed } = vi.hoisted(() => ({
+  mockLogOrphanedFunctionCallFixed: vi.fn(),
+}));
+
+vi.mock('../telemetry/loggers.js', async (importOriginal) => {
+  const actual =
+    await importOriginal<typeof import('../telemetry/loggers.js')>();
+  return {
+    ...actual,
+    logOrphanedFunctionCallFixed: mockLogOrphanedFunctionCallFixed,
+  };
+});
+
+describe('GeminiChat History Repair', () => {
+  let chat: GeminiChat;
+  let mockConfig: Config;
+
+  beforeEach(() => {
+    vi.clearAllMocks();
+
+    mockConfig = {
+      getSessionId: () => 'test-session-id',
+      getTelemetryLogPromptsEnabled: () => true,
+      getUsageStatisticsEnabled: () => true,
+      getDebugMode: () => false,
+      getPreviewFeatures: () => false,
+      getContentGeneratorConfig: vi.fn().mockImplementation(() => ({
+        authType: 'oauth-personal',
+        model: 'gemini-pro',
+      })),
+      getModel: vi.fn().mockReturnValue('gemini-pro'),
+      getProjectRoot: vi.fn().mockReturnValue('/test/project/root'),
+      storage: {
+        getProjectTempDir: vi.fn().mockReturnValue('/test/temp'),
+      },
+      getToolRegistry: vi.fn().mockReturnValue({
+        getTool: vi.fn(),
+      }),
+      modelConfigService: {
+        getResolvedConfig: vi.fn().mockImplementation((modelConfigKey) => {
+          const model = modelConfigKey.model ?? 'gemini-pro';
+          return {
+            model,
+            generateContentConfig: {
+              temperature: 0,
+              thinkingConfig: {
+                thinkingBudget: DEFAULT_THINKING_MODE,
+              },
+            },
+          };
+        }),
+      },
+      getActiveModel: vi.fn().mockReturnValue('gemini-pro'),
+      getModelAvailabilityService: vi
+        .fn()
+        .mockReturnValue(createAvailabilityServiceMock()),
+      getMessageBus: vi.fn().mockReturnValue(createMockMessageBus()),
+    } as unknown as Config;
+
+    chat = new GeminiChat(mockConfig);
+  });
+
+  describe('ensureActiveLoopHasFunctionResponses', () => {
+    it('should add synthetic function responses for missing responses in the history', () => {
+      const history: Content[] = [
+        { role: 'user', parts: [{ text: 'Start' }] },
+        {
+          role: 'model',
+          parts: [
+            { functionCall: { name: 'tool1', args: {} } },
+            { functionCall: { name: 'tool2', args: {} } },
+          ],
+        },
+      ];
+
+      const newContents = chat.ensureActiveLoopHasFunctionResponses(
+        history,
+        'test-model',
+      );
+
+      expect(newContents.length).toBe(3);
+      expect(newContents[2].role).toBe('user');
+      expect(newContents[2].parts?.length).toBe(2);
+      expect(newContents[2].parts![0].functionResponse?.name).toBe('tool1');
+      expect(newContents[2].parts![1].functionResponse?.name).toBe('tool2');
+      expect(newContents[2].parts![0].functionResponse?.response).toEqual({
+        status: 'unknown',
+        message: expect.stringContaining('unknown'),
+      });
+      expect(mockLogOrphanedFunctionCallFixed).toHaveBeenCalledTimes(2);
+    });
+
+    it('should add missing responses to existing user turn', () => {
+      const history: Content[] = [
+        { role: 'user', parts: [{ text: 'Start' }] },
+        {
+          role: 'model',
+          parts: [{ functionCall: { name: 'tool1', args: {} } }],
+        },
+        {
+          role: 'user',
+          parts: [{ text: 'Some other user message' }],
+        },
+      ];
+
+      const newContents = chat.ensureActiveLoopHasFunctionResponses(
+        history,
+        'test-model',
+      );
+
+      expect(newContents.length).toBe(3);
+      expect(newContents[2].role).toBe('user');
+      expect(newContents[2].parts?.length).toBe(2);
+      expect(newContents[2].parts![0].functionResponse?.name).toBe('tool1');
+      expect(newContents[2].parts![1].text).toBe('Some other user message');
+      expect(mockLogOrphanedFunctionCallFixed).toHaveBeenCalled();
+    });
+
+    it('should match responses by ID if provided', () => {
+      const history: Content[] = [
+        { role: 'user', parts: [{ text: 'Start' }] },
+        {
+          role: 'model',
+          parts: [{ functionCall: { name: 'tool1', args: {}, id: 'call-1' } }],
+        },
+        {
+          role: 'user',
+          parts: [
+            {
+              functionResponse: {
+                name: 'tool1',
+                id: 'call-1',
+                response: { result: 'ok' },
+              },
+            },
+          ],
+        },
+      ];
+
+      const newContents = chat.ensureActiveLoopHasFunctionResponses(
+        history,
+        'test-model',
+      );
+
+      expect(newContents).toEqual(history);
+      expect(mockLogOrphanedFunctionCallFixed).not.toHaveBeenCalled();
+    });
+
+    it('should add synthetic response if ID does not match', () => {
+      const history: Content[] = [
+        { role: 'user', parts: [{ text: 'Start' }] },
+        {
+          role: 'model',
+          parts: [{ functionCall: { name: 'tool1', args: {}, id: 'call-1' } }],
+        },
+        {
+          role: 'user',
+          parts: [
+            {
+              functionResponse: {
+                name: 'tool1',
+                id: 'call-wrong',
+                response: { result: 'ok' },
+              },
+            },
+          ],
+        },
+      ];
+
+      const newContents = chat.ensureActiveLoopHasFunctionResponses(
+        history,
+        'test-model',
+      );
+
+      expect(newContents[2].parts?.length).toBe(2);
+      expect(newContents[2].parts![0].functionResponse?.id).toBe('call-1');
+      expect(newContents[2].parts![1].functionResponse?.id).toBe('call-wrong');
+      expect(mockLogOrphanedFunctionCallFixed).toHaveBeenCalled();
+    });
+
+    it('should repair history regardless of "active loop" interruptions', () => {
+      const history: Content[] = [
+        {
+          role: 'model',
+          parts: [{ functionCall: { name: 'old_tool', args: {} } }],
+        },
+        { role: 'user', parts: [{ text: 'Start' }] },
+        {
+          role: 'model',
+          parts: [{ functionCall: { name: 'new_tool', args: {} } }],
+        },
+      ];
+
+      const newContents = chat.ensureActiveLoopHasFunctionResponses(
+        history,
+        'test-model',
+      );
+
+      expect(newContents.length).toBe(4);
+      expect(newContents[1].parts![0].functionResponse?.name).toBe('old_tool');
+      expect(newContents[3].parts![0].functionResponse?.name).toBe('new_tool');
+      expect(mockLogOrphanedFunctionCallFixed).toHaveBeenCalledTimes(2);
+    });
+  });
+
+  describe('ensureActiveLoopHasThoughtSignatures', () => {
+    it('should add thoughtSignature to the first functionCall in each model turn of the active loop', () => {
+      const history: Content[] = [
+        { role: 'user', parts: [{ text: 'Old message' }] },
+        {
+          role: 'model',
+          parts: [{ functionCall: { name: 'old_tool', args: {} } }],
+        },
+        { role: 'user', parts: [{ text: 'Find a restaurant' }] }, // active loop starts here
+        {
+          role: 'model',
+          parts: [
+            { functionCall: { name: 'find_restaurant', args: {} } },
+            { functionCall: { name: 'find_restaurant_2', args: {} } },
+          ],
+        },
+        {
+          role: 'user',
+          parts: [
+            { functionResponse: { name: 'find_restaurant', response: {} } },
+          ],
+        },
+        {
+          role: 'model',
+          parts: [
+            {
+              functionCall: { name: 'tool_with_sig', args: {} },
+              thoughtSignature: 'existing-sig',
+            },
+            { functionCall: { name: 'another_tool', args: {} } },
+          ],
+        },
+      ];
+
+      const newContents = chat.ensureActiveLoopHasThoughtSignatures(history);
+
+      // Outside active loop - unchanged
+      expect(newContents[1]?.parts?.[0]).not.toHaveProperty('thoughtSignature');
+
+      // Inside active loop, first model turn
+      expect(newContents[3]?.parts?.[0]?.thoughtSignature).toBe(
+        SYNTHETIC_THOUGHT_SIGNATURE,
+      );
+      expect(newContents[3]?.parts?.[1]).not.toHaveProperty('thoughtSignature');
+
+      // Inside active loop, second model turn (already has sig)
+      expect(newContents[5]?.parts?.[0]?.thoughtSignature).toBe('existing-sig');
+      expect(newContents[5]?.parts?.[1]).not.toHaveProperty('thoughtSignature');
+    });
+
+    it('should not modify contents if there is no user text message', () => {
+      const history: Content[] = [
+        {
+          role: 'user',
+          parts: [{ functionResponse: { name: 'tool1', response: {} } }],
+        },
+        {
+          role: 'model',
+          parts: [{ functionCall: { name: 'tool2', args: {} } }],
+        },
+      ];
+      const newContents = chat.ensureActiveLoopHasThoughtSignatures(history);
+      expect(newContents).toEqual(history);
+    });
+  });
+});
diff --git a/packages/core/src/telemetry/loggers.ts b/packages/core/src/telemetry/loggers.ts
index ae25424464..16f57ab360 100644
--- a/packages/core/src/telemetry/loggers.ts
+++ b/packages/core/src/telemetry/loggers.ts
@@ -53,6 +53,7 @@ import type {
   HookCallEvent,
   StartupStatsEvent,
   LlmLoopCheckEvent,
+  OrphanedFunctionCallFixedEvent,
 } from './types.js';
 import {
   recordApiErrorMetrics,
@@ -719,6 +720,20 @@ export function logHookCall(config: Config, event: HookCallEvent): void {
   });
 }
 
+export function logOrphanedFunctionCallFixed(
+  config: Config,
+  event: OrphanedFunctionCallFixedEvent,
+): void {
+  bufferTelemetryEvent(() => {
+    const logger = logs.getLogger(SERVICE_NAME);
+    const logRecord: LogRecord = {
+      body: event.toLogBody(),
+      attributes: event.toOpenTelemetryAttributes(config),
+    };
+    logger.emit(logRecord);
+  });
+}
+
 export function logStartupStats(
   config: Config,
   event: StartupStatsEvent,
diff --git a/packages/core/src/telemetry/types.ts b/packages/core/src/telemetry/types.ts
index eb7fc0096e..ee211427d2 100644
--- a/packages/core/src/telemetry/types.ts
+++ b/packages/core/src/telemetry/types.ts
@@ -1522,6 +1522,36 @@ export class LlmLoopCheckEvent implements BaseTelemetryEvent {
   }
 }
 
+export const EVENT_ORPHANED_FUNCTION_CALL_FIXED =
+  'gemini_cli.chat.orphaned_function_call_fixed';
+export class OrphanedFunctionCallFixedEvent implements BaseTelemetryEvent {
+  'event.name': 'orphaned_function_call_fixed';
+  'event.timestamp': string;
+  model: string;
+  function_name: string;
+
+  constructor(model: string, function_name: string) {
+    this['event.name'] = 'orphaned_function_call_fixed';
+    this['event.timestamp'] = new Date().toISOString();
+    this.model = model;
+    this.function_name = function_name;
+  }
+
+  toOpenTelemetryAttributes(config: Config): LogAttributes {
+    return {
+      ...getCommonAttributes(config),
+      'event.name': EVENT_ORPHANED_FUNCTION_CALL_FIXED,
+      'event.timestamp': this['event.timestamp'],
+      model: this.model,
+      function_name: this.function_name,
+    };
+  }
+
+  toLogBody(): string {
+    return `Orphaned function call fixed for ${this.function_name}.`;
+  }
+}
+
 export type TelemetryEvent =
   | StartSessionEvent
   | EndSessionEvent
@@ -1555,7 +1585,8 @@ export type TelemetryEvent =
   | StartupStatsEvent
   | WebFetchFallbackAttemptEvent
   | EditStrategyEvent
-  | EditCorrectionEvent;
+  | EditCorrectionEvent
+  | OrphanedFunctionCallFixedEvent;
 
 export const EVENT_EXTENSION_DISABLE = 'gemini_cli.extension_disable';
 export class ExtensionDisableEvent implements BaseTelemetryEvent {