Heh heh.. It was kind of both.
As far as we known both Nightcrawler + "mysterious off camera man" are bad guys and we are certain that there are 2 badguys and 5 lackeys in the transport with a hostage. If we attack now, the chances of Phase being rescued are extremely slim now since Nightcrawler has us beat mobility wise. Making things worse, NC could theoretically take out our injured during the middle of the battle (via teliport + death drop).
If we follow NC and MOCM, there is always a chance that we could single them out if they are badguys then take a hostage of our own. Also, if they are leading us into a trap, at least they aren't springing it on us when are in the middle of a fight.
However, since NC was a student as at the school (as Cyclops mentioned when Miranda wasn't around), there is a chance he could have switched sides due to the student death's if Pyro's previous statements about hearing that NC is actually a decent guy are true. But even if he did, there is no guarantee that he would help us out if we attack the transport (especially if he doesn't want the badguys to know that he was about to betray them).
With that said, it's probably safer to see what NC has to offer (and then beat him up if he tries to trick us).
Also, Miranda's sense motive is +4, so there is a good chance she would fall for any of his bluffs.