How do you engage the flagship?

[Ralzar]

I finally got to the final zone for the first time and got really frustrated. Whenever I tried to get into combat with the flagship, I just wound up fighting a normal rebel ship instead. I must be missing something here. I tried to travel to where the flagship was, and it wasn't there any more, so I figured I had to anticipate where it was heading, but that didn't help either.
So in the end I just died from fighting normal rebel ships, never even getting to see what the flagship looked like. What am I doing wrong?

[TheAzryte]

The flagship jumps once everytime you jump twice. When it's jumping you'll see it moving on a line to another beacon on you map, so if it's orbiting a beacon, it'll be there when you jump there, if it's flying off and there's a line to another beacon, jump to that beacon instead as it will be there when you arrive.