It's a quote from the TV drama Manifest. Here are the lines:
-Per protocol, climbing to penetration altitude.
-Per protocol, adjusting flight path to storm center.
The drama is about a bunch of passengers and crew of a commercial airliner who suddenly reappear after being presumed dead for over five years.
The plane captain as the speaker of this line is trying to fly up to the sky and looking for some dark lightning to prove his own theory. What confused me is the meaning of per protocol. It seems like a regular term of airplane.