Well I have multiple ideas in mind really, in short the basics are either;
Option one; Mystery man has a direct hand or does not, in events leading to the two teams being captured, or at least one of the two, and then the other one or two teams bust them out. Then things procead to plan.
Option Two; the fire teams get a sudden change in orders, based on what Noburu or at least the recon team finds, and they decide to assassinate the key targets and destory the labs, ignoring the reserve forces.
Option Three; we do a major timeskip to where the operations are on going and everything spirals out of control, forcing the teams to link up.
Option Four; is either by killing, IC incapacitation, or transfering, the inactives are switched out to another mission in the area and the teams have to change the plan.
Or some combination of them all really, its just bare basics atm that I can expand upon tomorrow if given some options or opinions at least. Either way I think the Army has two agenda's here, one is the hidden agenda the head mistress doesn't know of, that is the hidden cabal group within and without the army thats using the rebels as pawns, and the internal politics wanting to present a situation to test a weapons new power setting option (Isra), and then there is the honest stated Agenda.
If its an inside job then they'll want to arrange a situation so they can demand release authority. And on the other hand, while these rebels depend heavily on the group my Mystery man represents, they would likely attempt to watch things themselves.
The only problem with the capture option is short of escapee's I don't see them going along without taking significant damage, or being gassed when they sleep, and the orders one is kinda a FUBAR situation.
@ScarletNova