As far as I'm aware the single player campaign ends with Trent defeating the nomads and saving Sirius. If that is so what would justify the nomads becoming a threat again? If they were defeated by the Order once, would they not easily be subject to defeat again, considering humanity knows a lot more about them now?
I'm speaking about direct physical threat, not subterfuge from infected agents. I also vaguely remember that the big nomad battleships actually used a Wilde space shipyard to be constructed in the campaign.