In the mission "Drawn In", it says increase threat by 3 at the start of each status phase after round five. Does that mean increase threat by 3 in addition to the current threat level or increase by 3 in place of the current threat level?

Its a mission rule so its in addition to the regular threat increase.

It is in addition to the standard amount of threat. Otherwise it would say something like 'The threat level is 3 for the remainder of the mission.'

That's what I thought, thanks for the quick replies.