Oh, there's no doubt that there are secret ultra high tech stuff out there that could be considered UFOs. That's hardly new and some of the stuff on the horizon will make the Blackbird and stealth aircraft look like child's play. There are likely weapons in development will eventually make rail guns obsolete.
Could they take over the planet? Nah. I don't expect anything like that to happen. They'd rather just keep the current gravy train rolling. There's a sheet ton of money in defense contracting, so there's really no need to rock the boat too much.