diff --git a/commands/security/analyze.toml b/commands/security/analyze.toml
index cde5ded..d8f1eab 100644
--- a/commands/security/analyze.toml
+++ b/commands/security/analyze.toml
@@ -108,7 +108,8 @@ Your first action is to create a `SECURITY_ANALYSIS_TODO.md` file with the follo
 You will now begin executing the plan. The following are your precise instructions to start with.
 
 1.  **To complete the 'Define the audit scope' task:**
-    *   You **MUST** use the `get_audit_scope` tool and nothing else to get a list of changed files to perform a security scan on. 
+    *   Identify if the user specified specific branches to compare (e.g. "compare main and dev").
+    *   You **MUST** use the `get_audit_scope` tool and nothing else to get a list of changed files to perform a security scan on. Pass the branch names as arguments if the user provided them; otherwise call it with no arguments to scan the current changes.
     *   After using the tool, provide the user a list of changed files. If the list of files is empty, ask the user to provide files to be scanned.
 
 2.  **Immediately after defining the scope, you must refine your plan:**
diff --git a/mcp-server/src/filesystem.test.ts b/mcp-server/src/filesystem.test.ts
index 7af19d5..c3cd1e1 100644
--- a/mcp-server/src/filesystem.test.ts
+++ b/mcp-server/src/filesystem.test.ts
@@ -12,24 +12,58 @@ import * as fs from 'fs';
 describe('filesystem', () => {
   beforeAll(() => {
     execSync('git init');
-    execSync('git remote add origin https://github.com/gemini-testing/gemini-test-repo.git');
     fs.writeFileSync('test.txt', 'hello');
     execSync('git add .');
     execSync('git commit -m "initial commit"');
   });
 
   afterAll(() => {
-    fs.unlinkSync('test.txt');
+    // Cleanup created files and git repository if they exist for all tests
+    if (fs.existsSync('test.txt')) fs.unlinkSync('test.txt');
+    if (fs.existsSync('branch-test.txt')) fs.unlinkSync('branch-test.txt');
     execSync('rm -rf .git');
   });
 
   it('should return true if the directory is a github repository', () => {
+    // Setup: Add remote specifically for this test
+    execSync('git remote add origin https://github.com/gemini-testing/gemini-test-repo.git');
+    
     expect(isGitHubRepository()).toBe(true);
+    
+    // Cleanup: Remove remote so it doesn't affect other tests
+    execSync('git remote remove origin');
   });
 
-  it('should return a diff of the current changes', () => {
+  it('should return a diff of the current changes when no branches or commits are specified', () => {
     fs.writeFileSync('test.txt', 'hello world');
+    // Defaults to 'git diff' with remote removed
     const diff = getAuditScope();
     expect(diff).toContain('hello world');
   });
+
+  it('should return a diff between two specific branches', () => {
+    // 1. Base branch with specific content
+    execSync('git checkout -b pre');
+    fs.writeFileSync('branch-test.txt', 'pre content');
+    execSync('git add .');
+    execSync('git commit -m "pre branch commit"');
+
+    // 2. Head branch with the content modified
+    execSync('git checkout -b post');
+    fs.writeFileSync('branch-test.txt', 'post content');
+    execSync('git add .');
+    execSync('git commit -m "post branch commit"');
+
+    // 3. Compare them using the new arguments
+    const diff = getAuditScope('pre', 'post');
+
+    // 4. Verify the diff output
+    expect(diff).toContain('diff --git a/branch-test.txt b/branch-test.txt');
+    // FIXED: Updated expectations to match the actual file content
+    expect(diff).toContain('-pre content');
+    expect(diff).toContain('+post content');
+
+    // Cleanup by switching back to the main, so other tests aren't affected
+    execSync('git checkout master || git checkout main');
+  });
 });
diff --git a/mcp-server/src/filesystem.ts b/mcp-server/src/filesystem.ts
index d3850a1..af51c3f 100644
--- a/mcp-server/src/filesystem.ts
+++ b/mcp-server/src/filesystem.ts
@@ -27,13 +27,28 @@ export const isGitHubRepository = (): boolean => {
 };
 
 /**
- * Gets a changelist of the repository 
+ * Gets a changelist of the repository between two commits.
+ * Can compare between two commits, or get the diff of the working directory.
+ * If no commits are provided, it gets the changelist of the working directory.
+ * @param base The base commit branch or hash.
+ * @param head The head commit branch or hash.
+ * @returns The changelist as a string.
  */
-export function getAuditScope(): string {
-    let command = isGitHubRepository() ? 'git diff --merge-base origin/HEAD' : 'git diff';
+export function getAuditScope(base?: string, head?: string): string {
+    // Default to working directory diff if no commits are provided
+    const args: string[] = ["diff"];
+
+    // Add commit range if both base and head are provided
+    if (base !== undefined && head !== undefined) {
+        args.push(base, head);
+    }
+    // Otherwise, if this is a GitHub repository, use origin/HEAD as the base
+    else if (isGitHubRepository()) {
+        args.push('--merge-base', 'origin/HEAD');
+    }
     try {
         const diff = (
-        spawnSync('git', command.split(' ').slice(1), {
+        spawnSync('git', args, {
             encoding: 'utf-8',
         }).stdout || ''
         ).trim();
diff --git a/mcp-server/src/index.ts b/mcp-server/src/index.ts
index 4e85832..2ebd816 100644
--- a/mcp-server/src/index.ts
+++ b/mcp-server/src/index.ts
@@ -37,10 +37,13 @@ server.tool(
 
 server.tool(
   'get_audit_scope',
-  'Checks if the current directory is a GitHub repository.',
-  {},
-  () => {
-    const diff = getAuditScope();
+  'Gets the git diff of the current changes. Can optionally compare two specific branches.',
+  {
+    base: z.string().optional().describe('The base branch or commit hash (e.g., "main").'),
+    head: z.string().optional().describe('The head branch or commit hash (e.g., "feature-branch").'),
+  } as any,
+  ((args: { base?: string; head?: string }) => {
+    const diff = getAuditScope(args.base, args.head);
     return {
       content: [
         {
@@ -49,7 +52,7 @@ server.tool(
         },
       ],
     };
-  }
+  }) as any
 );
 
 server.tool(