It jumps in a zigzaggy pattern but heads towards the base. 2 jumps before it would get there, you lose if you've not attacked it once. right before it gets there, you lose if you've not attacked it twice. If it gets there and you don't show up at the same time to fight it for the 3rd time, you lose.
I imagine that the Flagship is doing what you've done all game: jumping around to look for good scrap opportunities before actually getting around to what the game says you should do.
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Simo-V - The Potential - Automated Scout - "Low O2" Icons
The Black Opal - The Asteroid - The Enforcer - The Pyro
