diff --git a/server/src/agents/pool/query.rs b/server/src/agents/pool/query.rs
index 8025ba4d..78318298 100644
--- a/server/src/agents/pool/query.rs
+++ b/server/src/agents/pool/query.rs
@@ -30,6 +30,19 @@ impl AgentPool {
             .collect())
     }
 
+    /// Return story IDs of merge jobs currently in the `Running` state.
+    ///
+    /// Used by `list_agents` and `get_pipeline_status` to surface in-flight
+    /// deterministic merges that hold the merge lock but have no agent entry.
+    pub fn list_running_merges(&self) -> Result<Vec<String>, String> {
+        let jobs = self.merge_jobs.lock().map_err(|e| e.to_string())?;
+        Ok(jobs
+            .values()
+            .filter(|job| matches!(job.status, crate::agents::merge::MergeJobStatus::Running))
+            .map(|job| job.story_id.clone())
+            .collect())
+    }
+
     /// List all agents with their status.
     pub fn list_agents(&self) -> Result<Vec<AgentInfo>, String> {
         let agents = self.agents.lock().map_err(|e| e.to_string())?;
diff --git a/server/src/http/mcp/agent_tools/mod.rs b/server/src/http/mcp/agent_tools/mod.rs
index ea59a27b..df3d5e03 100644
--- a/server/src/http/mcp/agent_tools/mod.rs
+++ b/server/src/http/mcp/agent_tools/mod.rs
@@ -87,25 +87,38 @@ pub(crate) async fn tool_stop_agent(args: &Value, ctx: &AppContext) -> Result<St
 pub(crate) fn tool_list_agents(ctx: &AppContext) -> Result<String, String> {
     let project_root = ctx.services.agents.get_project_root(&ctx.state).ok();
     let agents = ctx.services.agents.list_agents()?;
-    serde_json::to_string_pretty(&json!(
-        agents
-            .iter()
-            .filter(|a| {
-                project_root
-                    .as_deref()
-                    .map(|root| !crate::service::agents::is_archived(root, &a.story_id))
-                    .unwrap_or(true)
-            })
-            .map(|a| json!({
+    let mut entries: Vec<serde_json::Value> = agents
+        .iter()
+        .filter(|a| {
+            project_root
+                .as_deref()
+                .map(|root| !crate::service::agents::is_archived(root, &a.story_id))
+                .unwrap_or(true)
+        })
+        .map(|a| {
+            json!({
                 "story_id": a.story_id,
                 "agent_name": a.agent_name,
                 "status": a.status.to_string(),
                 "session_id": a.session_id,
                 "worktree_path": a.worktree_path,
-            }))
-            .collect::<Vec<_>>()
-    ))
-    .map_err(|e| format!("Serialization error: {e}"))
+            })
+        })
+        .collect();
+
+    // Append a synthetic entry for each deterministic merge holding the merge lock.
+    let running_merges = ctx.services.agents.list_running_merges()?;
+    for story_id in running_merges {
+        entries.push(json!({
+            "story_id": story_id,
+            "agent_name": "deterministic-merge",
+            "status": "Running",
+            "session_id": null,
+            "worktree_path": null,
+        }));
+    }
+
+    serde_json::to_string_pretty(&json!(entries)).map_err(|e| format!("Serialization error: {e}"))
 }
 
 /// Read agent session logs from disk and return a human-readable timeline.
diff --git a/server/src/http/mcp/story_tools/story.rs b/server/src/http/mcp/story_tools/story.rs
index bbd57d6e..373359a7 100644
--- a/server/src/http/mcp/story_tools/story.rs
+++ b/server/src/http/mcp/story_tools/story.rs
@@ -156,6 +156,7 @@ pub(crate) fn tool_list_upcoming(ctx: &AppContext) -> Result<String, String> {
 
 pub(crate) fn tool_get_pipeline_status(ctx: &AppContext) -> Result<String, String> {
     let state = load_pipeline_state(ctx)?;
+    let running_merges = ctx.services.agents.list_running_merges()?;
 
     fn map_items(items: &[crate::http::workflow::UpcomingStory], stage: &str) -> Vec<Value> {
         items
@@ -203,6 +204,7 @@ pub(crate) fn tool_get_pipeline_status(ctx: &AppContext) -> Result<String, Strin
         "active": active,
         "backlog": backlog,
         "backlog_count": backlog.len(),
+        "deterministic_merges_in_flight": running_merges,
     }))
     .map_err(|e| format!("Serialization error: {e}"))
 }