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I'm at the base trying to get a victory with the type B Rock ship, but the mothership is up in the right corner just jumping between 2 points ... not going towards the base. I waited like 10 times and it just keeps doing it.

Not very happy about this.

While at the base, I also get the message about the mothership only needing to stay there for three turns ... but I'm there, it's not.

WTH.
Could you upload the save so we can take a look?