diff --git a/navi/api/deps.py b/navi/api/deps.py
index 57bf3b4..02df568 100644
--- a/navi/api/deps.py
+++ b/navi/api/deps.py
@@ -99,8 +99,25 @@
 
 
 async def register_mcp_tools(registry: ToolRegistry, manager: McpManager) -> None:
-    """(kept for backward compat; MCP tools are already registered at startup)."""
-    pass
+    """Register all currently connected MCP tools into the tool registry."""
+    from navi.mcp.tools import McpTool
+
+    for name, client in manager.clients.items():
+        if not client.connected:
+            continue
+        try:
+            tools = await client.list_tools()
+            for tool in tools:
+                mcp_tool = McpTool(
+                    server_name=name,
+                    tool_name=tool.name,
+                    description=tool.description or "",
+                    parameters=tool.inputSchema,
+                    manager=manager,
+                )
+                registry.register_external(mcp_tool)
+        except Exception as exc:
+            log.warning("Failed to register MCP tools for %r: %s", name, exc)
 
 
 # Backward-compat re-exports so nothing outside breaks
diff --git a/navi/mcp/client.py b/navi/mcp/client.py
index 9807441..7d10f30 100644
--- a/navi/mcp/client.py
+++ b/navi/mcp/client.py
@@ -58,6 +58,10 @@
         if self._connected:
             return
 
+        # Ensure any stale transport/session from a prior disconnect or
+        # mark_disconnected() is fully torn down before we open fresh ones.
+        await self._cleanup()
+
         try:
             if self.config.is_stdio:
                 if not self.config.command:
@@ -134,6 +138,7 @@
         Used by the health-check loop when a server drops silently.
         """
         self._connected = False
+        self._session = None
 
     async def _cleanup(self) -> None:
         try: