diff --git a/src/geminimcp/server.py b/src/geminimcp/server.py
index e9db523..b2c7123 100644
--- a/src/geminimcp/server.py
+++ b/src/geminimcp/server.py
@@ -18,13 +18,6 @@ import shutil
 mcp = FastMCP("Gemini MCP Server-from guda.studio")
 
 
-def _empty_str_to_none(value: str | None) -> str | None:
-    """Convert empty strings to None for optional UUID parameters."""
-    if isinstance(value, str) and not value.strip():
-        return None
-    return value
-
-
 def run_shell_command(cmd: list[str]) -> Generator[str, None, None]:
     """Execute a command and stream its output line-by-line.
 
@@ -45,40 +38,64 @@ def run_shell_command(cmd: list[str]) -> Generator[str, None, None]:
 
     process = subprocess.Popen(
         popen_cmd,
-        shell=False,  # Safer: no shell injection
-        stdin=subprocess.PIPE,  # Prevent process from waiting for input
+        shell=False,
+        stdin=subprocess.DEVNULL,
         stdout=subprocess.PIPE,
         stderr=subprocess.STDOUT,
         universal_newlines=True,
-        encoding="utf-8",
+        encoding='utf-8',
     )
 
-    output_queue: queue.Queue[str] = queue.Queue()
+    output_queue: queue.Queue[str | None] = queue.Queue()
+    GRACEFUL_SHUTDOWN_DELAY = 0.3
+
+    def is_turn_completed(line: str) -> bool:
+        """Check if the line indicates turn completion via JSON parsing."""
+        try:
+            data = json.loads(line)
+            return data.get("type") == "turn.completed"
+        except (json.JSONDecodeError, AttributeError, TypeError):
+            return False
 
     def read_output() -> None:
         """Read process output in a separate thread."""
         if process.stdout:
             for line in iter(process.stdout.readline, ""):
-                output_queue.put(line.strip())
+                stripped = line.strip()
+                output_queue.put(stripped)
+                if is_turn_completed(stripped):
+                    time.sleep(GRACEFUL_SHUTDOWN_DELAY)
+                    process.terminate()
+                    break
             process.stdout.close()
+        output_queue.put(None)
 
     thread = threading.Thread(target=read_output)
-    thread.daemon = True
     thread.start()
 
     # Yield lines while process is running
-    while process.poll() is None:
+    while True:
         try:
-            yield output_queue.get(timeout=0.1)
+            line = output_queue.get(timeout=0.5)
+            if line is None:
+                break
+            yield line
         except queue.Empty:
-            continue
+            if process.poll() is not None and not thread.is_alive():
+                break
 
-    process.wait()
+    try:
+        process.wait(timeout=5)
+    except subprocess.TimeoutExpired:
+        process.kill()
+        process.wait()
+    thread.join(timeout=5)
 
-    # Drain remaining output from queue
     while not output_queue.empty():
         try:
-            yield output_queue.get_nowait()
+            line = output_queue.get_nowait()
+            if line is not None:
+                yield line
         except queue.Empty:
             break
 
@@ -194,9 +211,11 @@ async def gemini(
             #     err_message = "gemini error: " + line_dict.get("message", "")
         except json.JSONDecodeError as error:
             # Improved error handling: include problematic line
-            err_message = line
+            err_message += "\n\n[json decode error] " + line
+            continue
         except Exception as error:
-            err_message = f"Unexpected error: {error}. Line: {line!r}"
+            err_message += "\n\n[unexpected error] " + f"Unexpected error: {error}. Line: {line!r}"
+            break
 
 
     if thread_id is None:
@@ -205,10 +224,10 @@ async def gemini(
             "Failed to get `SESSION_ID` from the gemini session. \n\n" + err_message
         )
 
-    if len(agent_messages) == 0:
+    if success and len(agent_messages) == 0:
         success = False
         err_message = (
-            "Failed to get `agent_messages` from the gemini session. \n\n You can try to set `return_all_messages` to `True` to get the full information. \n\n "
+            "Failed to retrieve `agent_messages` data from the Gemini session. This might be due to Gemini performing a tool call. You can continue using the `SESSION_ID` to proceed with the conversation. \n\n "
             + err_message
         )
 
@@ -219,10 +238,11 @@ async def gemini(
             "agent_messages": agent_messages,
             # "PROMPT": PROMPT,
         }
-        if return_all_messages:
-            result["all_messages"] = all_messages
     else:
         result = {"success": False, "error": err_message}
+    
+    if return_all_messages:
+        result["all_messages"] = all_messages
 
     return result