diff --git a/shannon.mjs b/shannon.mjs
index 90cd839..4315256 100755
--- a/shannon.mjs
+++ b/shannon.mjs
@@ -25,6 +25,7 @@ import { assembleFinalReport } from './src/phases/reporting.js';
 
 // Utils
 import { timingResults, costResults, displayTimingSummary, Timer, formatDuration } from './src/utils/metrics.js';
+import { setupLogging } from './src/utils/logger.js';
 
 // CLI
 import { handleDeveloperCommand } from './src/cli/command-handler.js';
@@ -44,16 +45,21 @@ import {
 // Configure zx to disable timeouts (let tools run as long as needed)
 $.timeout = 0;
 
+// Global cleanup function for logging
+let cleanupLogging = null;
+
 // Setup graceful cleanup on process signals
 process.on('SIGINT', async () => {
   console.log(chalk.yellow('\n⚠️ Received SIGINT, cleaning up...'));
   await cleanupMCP();
+  if (cleanupLogging) await cleanupLogging();
   process.exit(0);
 });
 
 process.on('SIGTERM', async () => {
   console.log(chalk.yellow('\n⚠️ Received SIGTERM, cleaning up...'));
   await cleanupMCP();
+  if (cleanupLogging) await cleanupLogging();
   process.exit(0);
 });
 
@@ -377,6 +383,7 @@ if (args[0] && args[0].includes('shannon.mjs')) {
 // Parse flags and arguments
 let configPath = null;
 let pipelineTestingMode = false;
+let logFilePath = null;
 const nonFlagArgs = [];
 let developerCommand = null;
 const developerCommands = ['--run-phase', '--run-all', '--rollback-to', '--rerun', '--status', '--list-agents', '--cleanup'];
@@ -390,6 +397,16 @@ for (let i = 0; i < args.length; i++) {
       console.log(chalk.red('❌ --config flag requires a file path'));
       process.exit(1);
     }
+  } else if (args[i] === '--log') {
+    // --log can optionally take a file path, otherwise use default
+    if (i + 1 < args.length && !args[i + 1].startsWith('-')) {
+      logFilePath = args[i + 1];
+      i++; // Skip the next argument
+    } else {
+      // Generate default log filename with timestamp
+      const timestamp = new Date().toISOString().replace(/[:.]/g, '-').slice(0, -5);
+      logFilePath = `shannon-${timestamp}.log`;
+    }
   } else if (args[i] === '--pipeline-testing') {
     pipelineTestingMode = true;
   } else if (developerCommands.includes(args[i])) {
@@ -416,10 +433,25 @@ if (args.includes('--help') || args.includes('-h') || args.includes('help')) {
   process.exit(0);
 }
 
+// Setup logging if --log flag is present
+if (logFilePath) {
+  try {
+    cleanupLogging = await setupLogging(logFilePath);
+    const absoluteLogPath = path.isAbsolute(logFilePath)
+      ? logFilePath
+      : path.join(process.cwd(), logFilePath);
+    console.log(chalk.green(`📝 Logging enabled: ${absoluteLogPath}`));
+  } catch (error) {
+    console.log(chalk.yellow(`⚠️ Failed to setup logging: ${error.message}`));
+    console.log(chalk.gray('Continuing without logging...'));
+  }
+}
+
 // Handle developer commands
 if (developerCommand) {
   await handleDeveloperCommand(developerCommand, nonFlagArgs, pipelineTestingMode, runClaudePromptWithRetry, loadPrompt);
   await cleanupMCP();
+  if (cleanupLogging) await cleanupLogging();
   process.exit(0);
 }
 
@@ -470,6 +502,7 @@ try {
   console.log(chalk.green.bold('\n📄 FINAL REPORT AVAILABLE:'));
   console.log(chalk.cyan(finalReportPath));
   await cleanupMCP();
+  if (cleanupLogging) await cleanupLogging();
 } catch (error) {
   // Enhanced error boundary with proper logging
   if (error instanceof PentestError) {
@@ -490,5 +523,6 @@ try {
     }
   }
   await cleanupMCP();
+  if (cleanupLogging) await cleanupLogging();
   process.exit(1);
 }
\ No newline at end of file
diff --git a/src/cli/ui.js b/src/cli/ui.js
index c12a4c0..cea967e 100644
--- a/src/cli/ui.js
+++ b/src/cli/ui.js
@@ -21,6 +21,7 @@ export function showHelp() {
 
   console.log(chalk.yellow.bold('OPTIONS:'));
   console.log('  --config <file>      YAML configuration file for authentication and testing parameters');
+  console.log('  --log [file]         Capture all output to log file (default: shannon-<timestamp>.log)');
   console.log('  --pipeline-testing   Use minimal prompts for fast pipeline testing (creates minimal deliverables)\n');
 
   console.log(chalk.yellow.bold('DEVELOPER COMMANDS:'));
@@ -36,6 +37,7 @@ export function showHelp() {
   console.log('  # Normal mode - create new session');
   console.log('  ./shannon.mjs "https://example.com" "/path/to/local/repo"');
   console.log('  ./shannon.mjs "https://example.com" "/path/to/local/repo" --config auth.yaml');
+  console.log('  ./shannon.mjs "https://example.com" "/path/to/local/repo" --log pentest.log');
   console.log('  ./shannon.mjs "https://example.com" "/path/to/local/repo" --setup-only  # Setup only\n');
 
   console.log('  # Developer mode - operate on existing session');
diff --git a/src/utils/logger.js b/src/utils/logger.js
new file mode 100644
index 0000000..be285d4
--- /dev/null
+++ b/src/utils/logger.js
@@ -0,0 +1,126 @@
+import { fs } from 'zx';
+import { path } from 'zx';
+
+/**
+ * Strips ANSI escape codes from a string
+ * @param {string} str - String with ANSI codes
+ * @returns {string} Clean string without ANSI codes
+ */
+function stripAnsi(str) {
+  if (typeof str !== 'string') {
+    return str;
+  }
+
+  // Remove ANSI escape sequences
+  // This regex matches all common ANSI codes including:
+  // - Colors (e.g., \x1b[32m)
+  // - Cursor movement (e.g., \x1b[1;1H)
+  // - Screen clearing (e.g., \x1b[0J)
+  // - 256-color codes (e.g., \x1b[38;2;244;197;66m)
+  return str.replace(
+    // eslint-disable-next-line no-control-regex
+    /\x1b\[[0-9;]*[a-zA-Z]|\x1b\][0-9];.*?\x07|\x1b\[[\d;]*m/g,
+    ''
+  );
+}
+
+/**
+ * Sets up logging to capture all stdout and stderr to a file
+ * @param {string} logFilePath - Path to the log file
+ * @returns {Promise<Function>} Cleanup function to restore original streams
+ */
+export async function setupLogging(logFilePath) {
+  // Resolve to absolute path
+  const absoluteLogPath = path.isAbsolute(logFilePath)
+    ? logFilePath
+    : path.join(process.cwd(), logFilePath);
+
+  // Ensure the directory exists
+  await fs.ensureDir(path.dirname(absoluteLogPath));
+
+  // Create write stream for the log file
+  const logStream = fs.createWriteStream(absoluteLogPath, { flags: 'a' });
+
+  // Buffer for lines that might be overwritten (carriage return without newline)
+  let stdoutBuffer = '';
+  let stderrBuffer = '';
+
+  // Store original stdout/stderr write functions
+  const originalStdoutWrite = process.stdout.write.bind(process.stdout);
+  const originalStderrWrite = process.stderr.write.bind(process.stderr);
+
+  // Override stdout
+  process.stdout.write = function(chunk, encoding, callback) {
+    // Write colorized output to terminal
+    originalStdoutWrite(chunk, encoding, callback);
+
+    // Write plain text (without ANSI codes) to log file
+    const cleanChunk = stripAnsi(chunk.toString());
+
+    // Handle carriage returns - only log when we get a newline
+    if (cleanChunk.includes('\r') && !cleanChunk.includes('\n')) {
+      // Buffer this line - it will be overwritten in terminal
+      stdoutBuffer = cleanChunk.replace(/\r/g, '');
+    } else if (cleanChunk.includes('\n')) {
+      // Flush buffer if exists, then write the new line
+      if (stdoutBuffer) {
+        stdoutBuffer = ''; // Clear buffer without writing (it was overwritten)
+      }
+      logStream.write(cleanChunk);
+    } else {
+      // Normal write
+      logStream.write(cleanChunk);
+    }
+
+    return true;
+  };
+
+  // Override stderr
+  process.stderr.write = function(chunk, encoding, callback) {
+    // Write colorized output to terminal
+    originalStderrWrite(chunk, encoding, callback);
+
+    // Write plain text (without ANSI codes) to log file
+    const cleanChunk = stripAnsi(chunk.toString());
+
+    // Handle carriage returns - only log when we get a newline
+    if (cleanChunk.includes('\r') && !cleanChunk.includes('\n')) {
+      // Buffer this line - it will be overwritten in terminal
+      stderrBuffer = cleanChunk.replace(/\r/g, '');
+    } else if (cleanChunk.includes('\n')) {
+      // Flush buffer if exists, then write the new line
+      if (stderrBuffer) {
+        stderrBuffer = ''; // Clear buffer without writing (it was overwritten)
+      }
+      logStream.write(cleanChunk);
+    } else {
+      // Normal write
+      logStream.write(cleanChunk);
+    }
+
+    return true;
+  };
+
+  // Return cleanup function
+  return async function cleanup() {
+    // Restore original streams
+    process.stdout.write = originalStdoutWrite;
+    process.stderr.write = originalStderrWrite;
+
+    // Flush any remaining buffers
+    if (stdoutBuffer) {
+      logStream.write(stdoutBuffer + '\n');
+    }
+    if (stderrBuffer) {
+      logStream.write(stderrBuffer + '\n');
+    }
+
+    // Close the log stream
+    return new Promise((resolve, reject) => {
+      logStream.end((err) => {
+        if (err) reject(err);
+        else resolve();
+      });
+    });
+  };
+}