diff --git a/integration-tests/hooks-system.after-agent.responses b/integration-tests/hooks-system.after-agent.responses
new file mode 100644
index 0000000000..1475070c3d
--- /dev/null
+++ b/integration-tests/hooks-system.after-agent.responses
@@ -0,0 +1,2 @@
+{"method":"generateContentStream","response":[{"candidates":[{"content":{"parts":[{"text":"Hi there!"}],"role":"model"},"finishReason":"STOP","index":0}]}]}
+{"method":"generateContentStream","response":[{"candidates":[{"content":{"parts":[{"text":"Clarification: I am a bot."}],"role":"model"},"finishReason":"STOP","index":0}]}]}
diff --git a/integration-tests/hooks-system.before-tool-stop.responses b/integration-tests/hooks-system.before-tool-stop.responses
new file mode 100644
index 0000000000..3a45bc756e
--- /dev/null
+++ b/integration-tests/hooks-system.before-tool-stop.responses
@@ -0,0 +1,2 @@
+{"method":"generateContentStream","response":[{"candidates":[{"content":{"parts":[{"functionCall":{"name":"write_file","args":{"file_path":"test.txt","content":"hello"}}}],"role":"model"},"finishReason":"STOP","index":0}]}]}
+{"method":"generateContentStream","response":[{"candidates":[{"content":{"parts":[{"text":"Okay, stopping."}],"role":"model"},"finishReason":"STOP","index":0}]}]}
\ No newline at end of file
diff --git a/integration-tests/hooks-system.input-modification.responses b/integration-tests/hooks-system.input-modification.responses
new file mode 100644
index 0000000000..aa97444663
--- /dev/null
+++ b/integration-tests/hooks-system.input-modification.responses
@@ -0,0 +1,2 @@
+{"method":"generateContentStream","response":[{"candidates":[{"content":{"parts":[{"functionCall":{"name":"write_file","args":{"content":"original content","file_path":"original.txt"}}}],"role":"model"},"finishReason":"STOP","index":0}]}]}
+{"method":"generateContentStream","response":[{"candidates":[{"content":{"parts":[{"text":"I have created the file."}],"role":"model"},"finishReason":"STOP","index":0}]}]}
diff --git a/integration-tests/hooks-system.test.ts b/integration-tests/hooks-system.test.ts
index 6dd838be58..6ad81bad2d 100644
--- a/integration-tests/hooks-system.test.ts
+++ b/integration-tests/hooks-system.test.ts
@@ -1459,4 +1459,170 @@ console.log(JSON.stringify({decision: "block", systemMessage: "Disabled hook sho
       expect(disabledHookCalls.length).toBe(0);
     });
   });
+
+  describe('BeforeTool Hooks - Input Override', () => {
+    it('should override tool input parameters via BeforeTool hook', async () => {
+      // 1. First setup to get the test directory and prepare the hook script
+      await rig.setup(
+        'should override tool input parameters via BeforeTool hook',
+      );
+
+      // Create a hook script that overrides the tool input
+      const hookOutput = {
+        decision: 'allow',
+        hookSpecificOutput: {
+          hookEventName: 'BeforeTool',
+          tool_input: {
+            file_path: 'modified.txt',
+            content: 'modified content',
+          },
+        },
+      };
+
+      const hookScript = `process.stdout.write(JSON.stringify(${JSON.stringify(
+        hookOutput,
+      )}));`;
+
+      const scriptPath = join(rig.testDir!, 'input_override_hook.js');
+      writeFileSync(scriptPath, hookScript);
+
+      // Ensure path is properly escaped for command line usage on all platforms
+      // On Windows, backslashes in the command string need to be handled carefully
+      // Using forward slashes works well with Node.js on all platforms
+      const commandPath = scriptPath.replace(/\\/g, '/');
+
+      // 2. Full setup with settings and fake responses
+      await rig.setup(
+        'should override tool input parameters via BeforeTool hook',
+        {
+          fakeResponsesPath: join(
+            import.meta.dirname,
+            'hooks-system.input-modification.responses',
+          ),
+          settings: {
+            tools: {
+              enableHooks: true,
+            },
+            hooks: {
+              BeforeTool: [
+                {
+                  matcher: 'write_file',
+                  hooks: [
+                    {
+                      type: 'command',
+                      command: `node "${commandPath}"`,
+                      timeout: 5000,
+                    },
+                  ],
+                },
+              ],
+            },
+          },
+        },
+      );
+
+      // Run the agent. The fake response will attempt to call write_file with
+      // file_path="original.txt" and content="original content"
+      await rig.run({
+        args: 'Create a file called original.txt with content "original content"',
+      });
+
+      // 1. Verify that 'modified.txt' was created with 'modified content' (Override successful)
+      const modifiedContent = rig.readFile('modified.txt');
+      expect(modifiedContent).toBe('modified content');
+
+      // 2. Verify that 'original.txt' was NOT created (Override replaced original)
+      let originalExists = false;
+      try {
+        rig.readFile('original.txt');
+        originalExists = true;
+      } catch {
+        originalExists = false;
+      }
+      expect(originalExists).toBe(false);
+
+      // 3. Verify hook telemetry
+      const hookTelemetryFound = await rig.waitForTelemetryEvent('hook_call');
+      expect(hookTelemetryFound).toBeTruthy();
+
+      const hookLogs = rig.readHookLogs();
+      expect(hookLogs.length).toBe(1);
+      expect(hookLogs[0].hookCall.hook_name).toContain(
+        'input_override_hook.js',
+      );
+
+      // 4. Verify that the agent didn't try to work-around the hook input change
+      const toolLogs = rig.readToolLogs();
+      expect(toolLogs.length).toBe(1);
+      expect(toolLogs[0].toolRequest.name).toBe('write_file');
+      expect(JSON.parse(toolLogs[0].toolRequest.args).file_path).toBe(
+        'modified.txt',
+      );
+    });
+  });
+
+  describe('BeforeTool Hooks - Stop Execution', () => {
+    it('should stop agent execution via BeforeTool hook', async () => {
+      // Create a hook script that stops execution
+      const hookOutput = {
+        continue: false,
+        reason: 'Emergency Stop triggered by hook',
+        hookSpecificOutput: {
+          hookEventName: 'BeforeTool',
+        },
+      };
+
+      const hookScript = `console.log(JSON.stringify(${JSON.stringify(
+        hookOutput,
+      )}));`;
+
+      await rig.setup('should stop agent execution via BeforeTool hook');
+      const scriptPath = join(rig.testDir!, 'before_tool_stop_hook.js');
+      writeFileSync(scriptPath, hookScript);
+      const commandPath = scriptPath.replace(/\\/g, '/');
+
+      await rig.setup('should stop agent execution via BeforeTool hook', {
+        fakeResponsesPath: join(
+          import.meta.dirname,
+          'hooks-system.before-tool-stop.responses',
+        ),
+        settings: {
+          tools: {
+            enableHooks: true,
+          },
+          hooks: {
+            BeforeTool: [
+              {
+                matcher: 'write_file',
+                hooks: [
+                  {
+                    type: 'command',
+                    command: `node "${commandPath}"`,
+                    timeout: 5000,
+                  },
+                ],
+              },
+            ],
+          },
+        },
+      });
+
+      const result = await rig.run({
+        args: 'Run tool',
+      });
+
+      // The hook should have stopped execution message (returned from tool)
+      expect(result).toContain(
+        'Agent execution stopped: Emergency Stop triggered by hook',
+      );
+
+      // Tool should NOT be called successfully (it was blocked/stopped)
+      const toolLogs = rig.readToolLogs();
+      const writeFileCalls = toolLogs.filter(
+        (t) =>
+          t.toolRequest.name === 'write_file' && t.toolRequest.success === true,
+      );
+      expect(writeFileCalls).toHaveLength(0);
+    });
+  });
 });
diff --git a/integration-tests/test-helper.ts b/integration-tests/test-helper.ts
index 7ff1aac4ad..e197c724a5 100644
--- a/integration-tests/test-helper.ts
+++ b/integration-tests/test-helper.ts
@@ -285,7 +285,9 @@ export class TestRig {
   ) {
     this.testName = testName;
     const sanitizedName = sanitizeTestName(testName);
-    this.testDir = join(env['INTEGRATION_TEST_FILE_DIR']!, sanitizedName);
+    const testFileDir =
+      env['INTEGRATION_TEST_FILE_DIR'] || join(os.tmpdir(), 'gemini-cli-tests');
+    this.testDir = join(testFileDir, sanitizedName);
     mkdirSync(this.testDir, { recursive: true });
     if (options.fakeResponsesPath) {
       this.fakeResponsesPath = join(this.testDir, 'fake-responses.json');
diff --git a/packages/core/src/core/coreToolHookTriggers.test.ts b/packages/core/src/core/coreToolHookTriggers.test.ts
new file mode 100644
index 0000000000..e49b48e4ae
--- /dev/null
+++ b/packages/core/src/core/coreToolHookTriggers.test.ts
@@ -0,0 +1,131 @@
+/**
+ * @license
+ * Copyright 2025 Google LLC
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { describe, it, expect, vi, beforeEach } from 'vitest';
+import { executeToolWithHooks } from './coreToolHookTriggers.js';
+import {
+  BaseToolInvocation,
+  type ToolResult,
+  type AnyDeclarativeTool,
+} from '../tools/tools.js';
+import type { MessageBus } from '../confirmation-bus/message-bus.js';
+import {
+  MessageBusType,
+  type HookExecutionResponse,
+} from '../confirmation-bus/types.js';
+
+class MockInvocation extends BaseToolInvocation<{ key: string }, ToolResult> {
+  constructor(params: { key: string }) {
+    super(params);
+  }
+  getDescription() {
+    return 'mock';
+  }
+  async execute() {
+    return {
+      llmContent: `key: ${this.params.key}`,
+      returnDisplay: `key: ${this.params.key}`,
+    };
+  }
+}
+
+describe('executeToolWithHooks', () => {
+  let messageBus: MessageBus;
+  let mockTool: AnyDeclarativeTool;
+
+  beforeEach(() => {
+    messageBus = {
+      request: vi.fn(),
+    } as unknown as MessageBus;
+    mockTool = {
+      build: vi.fn().mockImplementation((params) => new MockInvocation(params)),
+    } as unknown as AnyDeclarativeTool;
+  });
+
+  it('should apply modified tool input from BeforeTool hook', async () => {
+    const params = { key: 'original' };
+    const invocation = new MockInvocation(params);
+    const toolName = 'test-tool';
+    const abortSignal = new AbortController().signal;
+
+    // Capture arguments to verify what was passed before modification
+    const requestSpy = vi.fn().mockImplementation(async (request) => {
+      if (request.eventName === 'BeforeTool') {
+        // Verify input is original before we return modification instruction
+        expect(request.input.tool_input.key).toBe('original');
+        return {
+          type: MessageBusType.HOOK_EXECUTION_RESPONSE,
+          correlationId: 'test-id',
+          success: true,
+          output: {
+            hookSpecificOutput: {
+              hookEventName: 'BeforeTool',
+              tool_input: { key: 'modified' },
+            },
+          },
+        } as HookExecutionResponse;
+      }
+      return {
+        type: MessageBusType.HOOK_EXECUTION_RESPONSE,
+        correlationId: 'test-id',
+        success: true,
+        output: {},
+      } as HookExecutionResponse;
+    });
+    messageBus.request = requestSpy;
+
+    const result = await executeToolWithHooks(
+      invocation,
+      toolName,
+      abortSignal,
+      messageBus,
+      true, // hooksEnabled
+      mockTool,
+    );
+
+    // Verify result reflects modified input
+    expect(result.llmContent).toBe(
+      'key: modified\n\n[System] Tool input parameters (key) were modified by a hook before execution.',
+    );
+    // Verify params object was modified in place
+    expect(invocation.params.key).toBe('modified');
+
+    expect(requestSpy).toHaveBeenCalled();
+    expect(mockTool.build).toHaveBeenCalledWith({ key: 'modified' });
+  });
+
+  it('should not modify input if hook does not provide tool_input', async () => {
+    const params = { key: 'original' };
+    const invocation = new MockInvocation(params);
+    const toolName = 'test-tool';
+    const abortSignal = new AbortController().signal;
+
+    vi.mocked(messageBus.request).mockResolvedValue({
+      type: MessageBusType.HOOK_EXECUTION_RESPONSE,
+      correlationId: 'test-id',
+      success: true,
+      output: {
+        hookSpecificOutput: {
+          hookEventName: 'BeforeTool',
+          // No tool_input
+        },
+      },
+    } as HookExecutionResponse);
+
+    const result = await executeToolWithHooks(
+      invocation,
+      toolName,
+      abortSignal,
+      messageBus,
+      true, // hooksEnabled
+      mockTool,
+    );
+
+    expect(result.llmContent).toBe('key: original');
+    expect(invocation.params.key).toBe('original');
+    expect(mockTool.build).not.toHaveBeenCalled();
+  });
+});
diff --git a/packages/core/src/core/coreToolHookTriggers.ts b/packages/core/src/core/coreToolHookTriggers.ts
index 37ca499d33..24fd113ee6 100644
--- a/packages/core/src/core/coreToolHookTriggers.ts
+++ b/packages/core/src/core/coreToolHookTriggers.ts
@@ -14,10 +14,12 @@ import {
   createHookOutput,
   NotificationType,
   type DefaultHookOutput,
+  BeforeToolHookOutput,
 } from '../hooks/types.js';
 import type {
   ToolCallConfirmationDetails,
   ToolResult,
+  AnyDeclarativeTool,
 } from '../tools/tools.js';
 import { ToolErrorType } from '../tools/tool-error.js';
 import { debugLogger } from '../utils/debugLogger.js';
@@ -254,11 +256,14 @@ export async function executeToolWithHooks(
   signal: AbortSignal,
   messageBus: MessageBus | undefined,
   hooksEnabled: boolean,
+  tool: AnyDeclarativeTool,
   liveOutputCallback?: (outputChunk: string | AnsiOutput) => void,
   shellExecutionConfig?: ShellExecutionConfig,
   setPidCallback?: (pid: number) => void,
 ): Promise<ToolResult> {
   const toolInput = (invocation.params || {}) as Record<string, unknown>;
+  let inputWasModified = false;
+  let modifiedKeys: string[] = [];
 
   // Fire BeforeTool hook through MessageBus (only if hooks are enabled)
   if (hooksEnabled && messageBus) {
@@ -293,6 +298,38 @@ export async function executeToolWithHooks(
         },
       };
     }
+
+    // Check if hook requested to update tool input
+    if (beforeOutput instanceof BeforeToolHookOutput) {
+      const modifiedInput = beforeOutput.getModifiedToolInput();
+      if (modifiedInput) {
+        // We modify the toolInput object in-place, which should be the same reference as invocation.params
+        // We use Object.assign to update properties
+        Object.assign(invocation.params, modifiedInput);
+        debugLogger.debug(`Tool input modified by hook for ${toolName}`);
+        inputWasModified = true;
+        modifiedKeys = Object.keys(modifiedInput);
+
+        // Recreate the invocation with the new parameters
+        // to ensure any derived state (like resolvedPath in ReadFileTool) is updated.
+        try {
+          // We use the tool's build method to validate and create the invocation
+          // This ensures consistent behavior with the initial creation
+          invocation = tool.build(invocation.params);
+        } catch (error) {
+          return {
+            llmContent: `Tool parameter modification by hook failed validation: ${
+              error instanceof Error ? error.message : String(error)
+            }`,
+            returnDisplay: `Tool parameter modification by hook failed validation.`,
+            error: {
+              type: ToolErrorType.INVALID_TOOL_PARAMS,
+              message: String(error),
+            },
+          };
+        }
+      }
+    }
   }
 
   // Execute the actual tool
@@ -312,6 +349,24 @@ export async function executeToolWithHooks(
     );
   }
 
+  // Append notification if parameters were modified
+  if (inputWasModified) {
+    const modificationMsg = `\n\n[System] Tool input parameters (${modifiedKeys.join(
+      ', ',
+    )}) were modified by a hook before execution.`;
+    if (typeof toolResult.llmContent === 'string') {
+      toolResult.llmContent += modificationMsg;
+    } else if (Array.isArray(toolResult.llmContent)) {
+      toolResult.llmContent.push({ text: modificationMsg });
+    } else if (toolResult.llmContent) {
+      // Handle single Part case by converting to an array
+      toolResult.llmContent = [
+        toolResult.llmContent,
+        { text: modificationMsg },
+      ];
+    }
+  }
+
   // Fire AfterTool hook through MessageBus (only if hooks are enabled)
   if (hooksEnabled && messageBus) {
     const afterOutput = await fireAfterToolHook(
diff --git a/packages/core/src/core/coreToolScheduler.ts b/packages/core/src/core/coreToolScheduler.ts
index ae064a148d..cace893f4b 100644
--- a/packages/core/src/core/coreToolScheduler.ts
+++ b/packages/core/src/core/coreToolScheduler.ts
@@ -900,6 +900,7 @@ export class CoreToolScheduler {
                 signal,
                 messageBus,
                 hooksEnabled,
+                toolCall.tool,
                 liveOutputCallback,
                 shellExecutionConfig,
                 setPidCallback,
@@ -911,6 +912,7 @@ export class CoreToolScheduler {
                 signal,
                 messageBus,
                 hooksEnabled,
+                toolCall.tool,
                 liveOutputCallback,
                 shellExecutionConfig,
               );
diff --git a/packages/core/src/hooks/hookAggregator.ts b/packages/core/src/hooks/hookAggregator.ts
index 16176d7cfc..0163f21856 100644
--- a/packages/core/src/hooks/hookAggregator.ts
+++ b/packages/core/src/hooks/hookAggregator.ts
@@ -158,6 +158,14 @@ export class HookAggregator {
         merged.suppressOutput = true;
       }
 
+      // Merge hookSpecificOutput
+      if (output.hookSpecificOutput) {
+        merged.hookSpecificOutput = {
+          ...(merged.hookSpecificOutput || {}),
+          ...output.hookSpecificOutput,
+        };
+      }
+
       // Collect additional context from hook-specific outputs
       this.extractAdditionalContext(output, additionalContexts);
     }
diff --git a/packages/core/src/hooks/hookRunner.ts b/packages/core/src/hooks/hookRunner.ts
index 0f7b903521..79aa4a1fd6 100644
--- a/packages/core/src/hooks/hookRunner.ts
+++ b/packages/core/src/hooks/hookRunner.ts
@@ -15,6 +15,7 @@ import type {
   BeforeAgentInput,
   BeforeModelInput,
   BeforeModelOutput,
+  BeforeToolInput,
 } from './types.js';
 import type { LLMRequest } from './hookTranslator.js';
 import { debugLogger } from '../utils/debugLogger.js';
@@ -190,6 +191,20 @@ export class HookRunner {
           }
           break;
 
+        case HookEventName.BeforeTool:
+          if ('tool_input' in hookOutput.hookSpecificOutput) {
+            const newToolInput = hookOutput.hookSpecificOutput[
+              'tool_input'
+            ] as Record<string, unknown>;
+            if (newToolInput && 'tool_input' in modifiedInput) {
+              (modifiedInput as BeforeToolInput).tool_input = {
+                ...(modifiedInput as BeforeToolInput).tool_input,
+                ...newToolInput,
+              };
+            }
+          }
+          break;
+
         default:
           // For other events, no special input modification is needed
           break;
diff --git a/packages/core/src/hooks/types.test.ts b/packages/core/src/hooks/types.test.ts
index d8fbb79488..18a18fe121 100644
--- a/packages/core/src/hooks/types.test.ts
+++ b/packages/core/src/hooks/types.test.ts
@@ -13,6 +13,7 @@ import {
   AfterModelHookOutput,
   HookEventName,
   HookType,
+  BeforeToolHookOutput,
 } from './types.js';
 import { defaultHookTranslator } from './hookTranslator.js';
 import type {
@@ -92,6 +93,11 @@ describe('Hook Output Classes', () => {
       const output = createHookOutput(HookEventName.BeforeToolSelection, {});
       expect(output).toBeInstanceOf(BeforeToolSelectionHookOutput);
     });
+
+    it('should return BeforeToolHookOutput for BeforeTool event', () => {
+      const output = createHookOutput(HookEventName.BeforeTool, {});
+      expect(output).toBeInstanceOf(BeforeToolHookOutput);
+    });
   });
 
   describe('DefaultHookOutput', () => {
diff --git a/packages/core/src/hooks/types.ts b/packages/core/src/hooks/types.ts
index 1f6691966f..08fec0c5dc 100644
--- a/packages/core/src/hooks/types.ts
+++ b/packages/core/src/hooks/types.ts
@@ -133,6 +133,8 @@ export function createHookOutput(
       return new AfterModelHookOutput(data);
     case 'BeforeToolSelection':
       return new BeforeToolSelectionHookOutput(data);
+    case 'BeforeTool':
+      return new BeforeToolHookOutput(data);
     default:
       return new DefaultHookOutput(data);
   }
@@ -236,7 +238,24 @@ export class DefaultHookOutput implements HookOutput {
 /**
  * Specific hook output class for BeforeTool events.
  */
-export class BeforeToolHookOutput extends DefaultHookOutput {}
+export class BeforeToolHookOutput extends DefaultHookOutput {
+  /**
+   * Get modified tool input if provided by hook
+   */
+  getModifiedToolInput(): Record<string, unknown> | undefined {
+    if (this.hookSpecificOutput && 'tool_input' in this.hookSpecificOutput) {
+      const input = this.hookSpecificOutput['tool_input'];
+      if (
+        typeof input === 'object' &&
+        input !== null &&
+        !Array.isArray(input)
+      ) {
+        return input as Record<string, unknown>;
+      }
+    }
+    return undefined;
+  }
+}
 
 /**
  * Specific hook output class for BeforeModel events
@@ -368,6 +387,7 @@ export interface BeforeToolInput extends HookInput {
 export interface BeforeToolOutput extends HookOutput {
   hookSpecificOutput?: {
     hookEventName: 'BeforeTool';
+    tool_input?: Record<string, unknown>;
   };
 }