When in the Travel Phase Actions Event, the IND Frigate no ships may leave this sector this phase, but the mission An Explosive Plan moves the SF ships. Does the frigate take priority and the mission moves without the ships, or does the mission take priority and move the ships with it?
I think the frigate overrides all movement, but I wanted to get some other opinions.
As a general rule of thumb, for all games, "Cannot" trumps "can". This case will be no exception 
Yes, but it could be argued that the mission's phase event triggers before the frigate's because it is an event and not a static status, more so because I had just read a forum discussion that said players choose the order the events occur in. I had adjusted my game board before noting the frigate ability and then had to undo it. Not a big deal, I was just hoping for some possible clarification on scenarios like this where I get caught in a logic loop.
I 100% understand where you are coming from. The Frigate certainly has an event icon, and you are correct that there are rules that players choose the order in which to resolve Event icons.
I had forgoten the Frigate was indeed an event icon. In light of that, I think you could very well argue that you could resolve the Mission's movement effect before putting the Frigates movement denial into effect for the rest of the Travel phase.