diff --git a/src/mcp/install-mcp-server.ts b/src/mcp/install-mcp-server.ts
index c107fc1fa..0a2e7b4cf 100644
--- a/src/mcp/install-mcp-server.ts
+++ b/src/mcp/install-mcp-server.ts
@@ -3,6 +3,7 @@ import { GITHUB_API_URL, GITHUB_SERVER_URL } from "../github/api/config";
 import type { GitHubContext } from "../github/context";
 import { isEntityContext } from "../github/context";
 import { Octokit } from "@octokit/rest";
+import type { AutoDetectedMode } from "../modes/detector";
 
 type PrepareConfigParams = {
   githubToken: string;
@@ -12,8 +13,8 @@ type PrepareConfigParams = {
   baseBranch: string;
   claudeCommentId?: string;
   allowedTools: string[];
+  mode: AutoDetectedMode;
   context: GitHubContext;
-  mode: "tag" | "agent";
 };
 
 async function checkActionsReadPermission(
@@ -65,8 +66,13 @@ export async function prepareMcpConfig(
   try {
     const allowedToolsList = allowedTools || [];
 
+    // Detect if we're in agent mode (explicit prompt provided)
     const isAgentMode = mode === "agent";
 
+    const hasGitHubCommentTools = allowedToolsList.some((tool) =>
+      tool.startsWith("mcp__github_comment__"),
+    );
+
     const hasGitHubMcpTools = allowedToolsList.some((tool) =>
       tool.startsWith("mcp__github__"),
     );
@@ -86,7 +92,7 @@ export async function prepareMcpConfig(
     // Include comment server:
     // - Always in tag mode (for updating Claude comments)
     // - Only with explicit tools in agent mode
-    const shouldIncludeCommentServer = !isAgentMode;
+    const shouldIncludeCommentServer = !isAgentMode || hasGitHubCommentTools;
 
     if (shouldIncludeCommentServer) {
       baseMcpConfig.mcpServers.github_comment = {
diff --git a/src/modes/agent/index.ts b/src/modes/agent/index.ts
index 9c3a7b2dd..4bcd4aaaf 100644
--- a/src/modes/agent/index.ts
+++ b/src/modes/agent/index.ts
@@ -135,8 +135,8 @@ export const agentMode: Mode = {
       baseBranch: baseBranch,
       claudeCommentId: undefined, // No tracking comment in agent mode
       allowedTools,
-      context,
       mode: "agent",
+      context,
     });
 
     // Build final claude_args with multiple --mcp-config flags
diff --git a/src/modes/tag/index.ts b/src/modes/tag/index.ts
index adcf6e8df..be7df091c 100644
--- a/src/modes/tag/index.ts
+++ b/src/modes/tag/index.ts
@@ -14,6 +14,7 @@ import { createPrompt, generateDefaultPrompt } from "../../create-prompt";
 import { isEntityContext } from "../../github/context";
 import type { PreparedContext } from "../../create-prompt/types";
 import type { FetchDataResult } from "../../github/data/fetcher";
+import { parseAllowedTools } from "../agent/parse-tools";
 
 /**
  * Tag mode implementation.
@@ -112,20 +113,10 @@ export const tagMode: Mode = {
 
     await createPrompt(tagMode, modeContext, githubData, context);
 
-    // Get our GitHub MCP servers configuration
-    const ourMcpConfig = await prepareMcpConfig({
-      githubToken,
-      owner: context.repository.owner,
-      repo: context.repository.repo,
-      branch: branchInfo.claudeBranch || branchInfo.currentBranch,
-      baseBranch: branchInfo.baseBranch,
-      claudeCommentId: commentId.toString(),
-      allowedTools: [],
-      context,
-      mode: "tag",
-    });
-
-    // Don't output mcp_config separately anymore - include in claude_args
+    const userClaudeArgs = process.env.CLAUDE_ARGS || "";
+    const userAllowedMCPTools = parseAllowedTools(userClaudeArgs).filter(
+      (tool) => tool.startsWith("mcp__github_"),
+    );
 
     // Build claude_args for tag mode with required tools
     // Tag mode REQUIRES these tools to function properly
@@ -141,6 +132,7 @@ export const tagMode: Mode = {
       "mcp__github_ci__get_ci_status",
       "mcp__github_ci__get_workflow_run_details",
       "mcp__github_ci__download_job_log",
+      ...userAllowedMCPTools,
     ];
 
     // Add git commands when not using commit signing
@@ -162,7 +154,18 @@ export const tagMode: Mode = {
       );
     }
 
-    const userClaudeArgs = process.env.CLAUDE_ARGS || "";
+    // Get our GitHub MCP servers configuration
+    const ourMcpConfig = await prepareMcpConfig({
+      githubToken,
+      owner: context.repository.owner,
+      repo: context.repository.repo,
+      branch: branchInfo.claudeBranch || branchInfo.currentBranch,
+      baseBranch: branchInfo.baseBranch,
+      claudeCommentId: commentId.toString(),
+      allowedTools: Array.from(new Set(tagModeTools)),
+      mode: "tag",
+      context,
+    });
 
     // Build complete claude_args with multiple --mcp-config flags
     let claudeArgs = "";
diff --git a/test/install-mcp-server.test.ts b/test/install-mcp-server.test.ts
index 987dd7c68..9d628504d 100644
--- a/test/install-mcp-server.test.ts
+++ b/test/install-mcp-server.test.ts
@@ -106,8 +106,8 @@ describe("prepareMcpConfig", () => {
       branch: "test-branch",
       baseBranch: "main",
       allowedTools: [],
-      context: mockContextWithSigning,
       mode: "tag",
+      context: mockContextWithSigning,
     });
 
     const parsed = JSON.parse(result);
@@ -130,8 +130,8 @@ describe("prepareMcpConfig", () => {
       branch: "test-branch",
       baseBranch: "main",
       allowedTools: ["mcp__github__create_issue", "mcp__github__create_pr"],
-      context: mockContext,
       mode: "tag",
+      context: mockContext,
     });
 
     const parsed = JSON.parse(result);
@@ -151,8 +151,8 @@ describe("prepareMcpConfig", () => {
       branch: "test-branch",
       baseBranch: "main",
       allowedTools: ["mcp__github_inline_comment__create_inline_comment"],
-      context: mockPRContext,
       mode: "tag",
+      context: mockPRContext,
     });
 
     const parsed = JSON.parse(result);
@@ -172,8 +172,8 @@ describe("prepareMcpConfig", () => {
       branch: "test-branch",
       baseBranch: "main",
       allowedTools: [],
-      context: mockContext,
       mode: "tag",
+      context: mockContext,
     });
 
     const parsed = JSON.parse(result);
@@ -193,8 +193,8 @@ describe("prepareMcpConfig", () => {
       branch: "test-branch",
       baseBranch: "main",
       allowedTools: [],
-      context: mockContextWithSigning,
       mode: "tag",
+      context: mockContextWithSigning,
     });
 
     const parsed = JSON.parse(result);
@@ -213,8 +213,8 @@ describe("prepareMcpConfig", () => {
       branch: "test-branch",
       baseBranch: "main",
       allowedTools: [],
-      context: mockContextWithSigning,
       mode: "tag",
+      context: mockContextWithSigning,
     });
 
     const parsed = JSON.parse(result);
@@ -231,8 +231,8 @@ describe("prepareMcpConfig", () => {
       branch: "test-branch",
       baseBranch: "main",
       allowedTools: [],
-      context: mockPRContext,
       mode: "tag",
+      context: mockPRContext,
     });
 
     const parsed = JSON.parse(result);
@@ -251,8 +251,8 @@ describe("prepareMcpConfig", () => {
       branch: "test-branch",
       baseBranch: "main",
       allowedTools: [],
-      context: mockContext,
       mode: "tag",
+      context: mockContext,
     });
 
     const parsed = JSON.parse(result);
@@ -269,8 +269,8 @@ describe("prepareMcpConfig", () => {
       branch: "test-branch",
       baseBranch: "main",
       allowedTools: [],
-      context: mockPRContext,
       mode: "tag",
+      context: mockPRContext,
     });
 
     const parsed = JSON.parse(result);