diff --git a/.story_kit/stories/archived/40_mcp_server_obeys_storykit_port.md b/.story_kit/stories/archived/40_mcp_server_obeys_storykit_port.md
new file mode 100644
index 0000000..bb7ced3
--- /dev/null
+++ b/.story_kit/stories/archived/40_mcp_server_obeys_storykit_port.md
@@ -0,0 +1,14 @@
+---
+name: MCP Server Obeys STORYKIT_PORT
+test_plan: approved
+---
+
+## User Story
+
+As a developer running the server on a non-default port, I want agent worktrees to automatically discover the correct MCP server URL, so that spawned agents can use MCP tools without manual .mcp.json edits.
+
+## Acceptance Criteria
+
+- [x] Agent worktrees inherit the correct port from the running server (via STORYKIT_PORT env var or default 3001)
+- [x] The .mcp.json in agent worktrees points to the actual server port, not a hardcoded value
+- [x] Existing behaviour (default port 3001) continues to work when STORYKIT_PORT is not set
diff --git a/server/src/agents.rs b/server/src/agents.rs
index 23bce61..bd821b0 100644
--- a/server/src/agents.rs
+++ b/server/src/agents.rs
@@ -111,12 +111,14 @@ fn agent_info_from_entry(story_id: &str, agent: &StoryAgent) -> AgentInfo {
 /// Manages concurrent story agents, each in its own worktree.
 pub struct AgentPool {
     agents: Arc<Mutex<HashMap<String, StoryAgent>>>,
+    port: u16,
 }
 
 impl AgentPool {
-    pub fn new() -> Self {
+    pub fn new(port: u16) -> Self {
         Self {
             agents: Arc::new(Mutex::new(HashMap::new())),
+            port,
         }
     }
 
@@ -188,7 +190,7 @@ impl AgentPool {
         });
 
         // Create worktree
-        let wt_info = worktree::create_worktree(project_root, story_id, &config).await?;
+        let wt_info = worktree::create_worktree(project_root, story_id, &config, self.port).await?;
 
         // Update with worktree info
         {
@@ -696,7 +698,7 @@ mod tests {
 
     #[tokio::test]
     async fn wait_for_agent_returns_immediately_if_completed() {
-        let pool = AgentPool::new();
+        let pool = AgentPool::new(3001);
         pool.inject_test_agent("s1", "bot", AgentStatus::Completed);
 
         let info = pool.wait_for_agent("s1", "bot", 1000).await.unwrap();
@@ -707,7 +709,7 @@ mod tests {
 
     #[tokio::test]
     async fn wait_for_agent_returns_immediately_if_failed() {
-        let pool = AgentPool::new();
+        let pool = AgentPool::new(3001);
         pool.inject_test_agent("s2", "bot", AgentStatus::Failed);
 
         let info = pool.wait_for_agent("s2", "bot", 1000).await.unwrap();
@@ -716,7 +718,7 @@ mod tests {
 
     #[tokio::test]
     async fn wait_for_agent_completes_on_done_event() {
-        let pool = AgentPool::new();
+        let pool = AgentPool::new(3001);
         let tx = pool.inject_test_agent("s3", "bot", AgentStatus::Running);
 
         // Send Done event after a short delay
@@ -741,7 +743,7 @@ mod tests {
 
     #[tokio::test]
     async fn wait_for_agent_times_out() {
-        let pool = AgentPool::new();
+        let pool = AgentPool::new(3001);
         pool.inject_test_agent("s4", "bot", AgentStatus::Running);
 
         let result = pool.wait_for_agent("s4", "bot", 50).await;
@@ -752,14 +754,14 @@ mod tests {
 
     #[tokio::test]
     async fn wait_for_agent_errors_for_nonexistent() {
-        let pool = AgentPool::new();
+        let pool = AgentPool::new(3001);
         let result = pool.wait_for_agent("no_story", "no_bot", 100).await;
         assert!(result.is_err());
     }
 
     #[tokio::test]
     async fn wait_for_agent_completes_on_stopped_status_event() {
-        let pool = AgentPool::new();
+        let pool = AgentPool::new(3001);
         let tx = pool.inject_test_agent("s5", "bot", AgentStatus::Running);
 
         let tx_clone = tx.clone();
diff --git a/server/src/http/context.rs b/server/src/http/context.rs
index 069269d..26d805b 100644
--- a/server/src/http/context.rs
+++ b/server/src/http/context.rs
@@ -23,7 +23,7 @@ impl AppContext {
             state: Arc::new(state),
             store: Arc::new(JsonFileStore::new(store_path).unwrap()),
             workflow: Arc::new(std::sync::Mutex::new(WorkflowState::default())),
-            agents: Arc::new(AgentPool::new()),
+            agents: Arc::new(AgentPool::new(3001)),
         }
     }
 }
diff --git a/server/src/main.rs b/server/src/main.rs
index f622916..b5e4570 100644
--- a/server/src/main.rs
+++ b/server/src/main.rs
@@ -50,7 +50,8 @@ async fn main() -> Result<(), std::io::Error> {
         JsonFileStore::from_path(PathBuf::from("store.json")).map_err(std::io::Error::other)?,
     );
     let workflow = Arc::new(std::sync::Mutex::new(WorkflowState::default()));
-    let agents = Arc::new(AgentPool::new());
+    let port = resolve_port();
+    let agents = Arc::new(AgentPool::new(port));
 
     let ctx = AppContext {
         state: app_state,
@@ -60,8 +61,6 @@ async fn main() -> Result<(), std::io::Error> {
     };
 
     let app = build_routes(ctx);
-
-    let port = resolve_port();
     let addr = format!("127.0.0.1:{port}");
 
     println!(
diff --git a/server/src/worktree.rs b/server/src/worktree.rs
index 75c7f6f..8af37b3 100644
--- a/server/src/worktree.rs
+++ b/server/src/worktree.rs
@@ -2,6 +2,15 @@ use crate::config::ProjectConfig;
 use std::path::{Path, PathBuf};
 use std::process::Command;
 
+/// Write a `.mcp.json` file in the given directory pointing to the MCP server
+/// at the given port.
+pub fn write_mcp_json(dir: &Path, port: u16) -> Result<(), String> {
+    let content = format!(
+        "{{\n  \"mcpServers\": {{\n    \"story-kit\": {{\n      \"type\": \"http\",\n      \"url\": \"http://localhost:{port}/mcp\"\n    }}\n  }}\n}}\n"
+    );
+    std::fs::write(dir.join(".mcp.json"), content).map_err(|e| format!("Write .mcp.json: {e}"))
+}
+
 #[derive(Debug, Clone)]
 #[allow(dead_code)]
 pub struct WorktreeInfo {
@@ -46,12 +55,14 @@ fn detect_base_branch(project_root: &Path) -> String {
 ///
 /// - Creates the worktree at `{project_root}-story-{story_id}` (sibling directory)
 ///   on branch `feature/story-{story_id}`.
+/// - Writes `.mcp.json` in the worktree pointing to the MCP server at `port`.
 /// - Runs setup commands from the config for each component.
 /// - If the worktree/branch already exists, reuses rather than errors.
 pub async fn create_worktree(
     project_root: &Path,
     story_id: &str,
     config: &ProjectConfig,
+    port: u16,
 ) -> Result<WorktreeInfo, String> {
     let wt_path = worktree_path(project_root, story_id);
     let branch = branch_name(story_id);
@@ -60,6 +71,7 @@ pub async fn create_worktree(
 
     // Already exists — reuse
     if wt_path.exists() {
+        write_mcp_json(&wt_path, port)?;
         run_setup_commands(&wt_path, config).await?;
         return Ok(WorktreeInfo {
             path: wt_path,
@@ -75,6 +87,7 @@ pub async fn create_worktree(
         .await
         .map_err(|e| format!("spawn_blocking: {e}"))??;
 
+    write_mcp_json(&wt_path, port)?;
     run_setup_commands(&wt_path, config).await?;
 
     Ok(WorktreeInfo {
@@ -205,6 +218,28 @@ async fn run_teardown_commands(wt_path: &Path, config: &ProjectConfig) -> Result
     Ok(())
 }
 
+async fn run_shell_command(cmd: &str, cwd: &Path) -> Result<(), String> {
+    let cmd = cmd.to_string();
+    let cwd = cwd.to_path_buf();
+
+    tokio::task::spawn_blocking(move || {
+        eprintln!("[worktree] Running: {cmd} in {}", cwd.display());
+        let output = Command::new("sh")
+            .args(["-c", &cmd])
+            .current_dir(&cwd)
+            .output()
+            .map_err(|e| format!("Run '{cmd}': {e}"))?;
+
+        if !output.status.success() {
+            let stderr = String::from_utf8_lossy(&output.stderr);
+            return Err(format!("Command '{cmd}' failed: {stderr}"));
+        }
+        Ok(())
+    })
+    .await
+    .map_err(|e| format!("spawn_blocking: {e}"))?
+}
+
 #[cfg(test)]
 mod tests {
     use super::*;
@@ -225,6 +260,22 @@ mod tests {
             .expect("git commit");
     }
 
+    #[test]
+    fn write_mcp_json_uses_given_port() {
+        let tmp = TempDir::new().unwrap();
+        write_mcp_json(tmp.path(), 4242).unwrap();
+        let content = std::fs::read_to_string(tmp.path().join(".mcp.json")).unwrap();
+        assert!(content.contains("http://localhost:4242/mcp"));
+    }
+
+    #[test]
+    fn write_mcp_json_default_port() {
+        let tmp = TempDir::new().unwrap();
+        write_mcp_json(tmp.path(), 3001).unwrap();
+        let content = std::fs::read_to_string(tmp.path().join(".mcp.json")).unwrap();
+        assert!(content.contains("http://localhost:3001/mcp"));
+    }
+
     #[test]
     fn create_worktree_after_stale_reference() {
         let tmp = TempDir::new().unwrap();
@@ -255,25 +306,3 @@ mod tests {
         assert!(wt_path.exists());
     }
 }
-
-async fn run_shell_command(cmd: &str, cwd: &Path) -> Result<(), String> {
-    let cmd = cmd.to_string();
-    let cwd = cwd.to_path_buf();
-
-    tokio::task::spawn_blocking(move || {
-        eprintln!("[worktree] Running: {cmd} in {}", cwd.display());
-        let output = Command::new("sh")
-            .args(["-c", &cmd])
-            .current_dir(&cwd)
-            .output()
-            .map_err(|e| format!("Run '{cmd}': {e}"))?;
-
-        if !output.status.success() {
-            let stderr = String::from_utf8_lossy(&output.stderr);
-            return Err(format!("Command '{cmd}' failed: {stderr}"));
-        }
-        Ok(())
-    })
-    .await
-    .map_err(|e| format!("spawn_blocking: {e}"))?
-}