In the scene where Eagle Eye scrambles the MQ-9 Reaper after Jerry, an F-16 scrambles to intercept. Eagle Eye then sends a signal to the F-16 to eject its pilot, which is exactly what happens. However, this is far from possible. In order to eject, the pilot must pull on the ejection handle, or pull down on the face curtain. This sets off an explosive in the catapult gun, which in turn launches the ejection seat into the air.

The ejection process is purely mechanical and chemical, to prevent exactly what happens in the film. There is simply absolutely no way to eject a pilot remotely. The only way the system works is if the pilot makes it work.