As stated in the post above, and in the post announcing the winner for the game-wide vote on the next plot arc to be completed first, the Transports are in control o the time traveling technology by having the Transport Pad in their hands and control. The Transports would need to decide (by majority or by those with enough power or great amounts of sneakiness) to hand over control to the New Initiative, since the framework of that relationship right now isn't controlling/dictating. The New Initiative has no past research team, they haven't seen this tech, they're unaware if the United Earth has anything like it, and their only control toward the Transports is their connection to the adequate power source.

It's not in their interest to be dictating events when it's still possible, as far as they know, for the Transports to be a group sent in by the United Earth to expose them and quietly eradicate their group for the greater good.

Having a group that mediates between the two is still useful, but Saul is free to ICly choose to have the Department change aim or presentation as best makes sense to him. What that accomplishes in game will be up to what he does, how fellow PCs act, and what reactions the New Initiative will have depending on the course of events.

Note again that with each Plot Arc completion, we're looking at a shift in landscape, and a shift in New Initiative mentality. They don't know this for sure ICly, but it's good to keep in mind OOCly that we're in an unstable time-frame, due to the fact that this presentation of Winter Wonderland is meant to change as soon as the Cloning/Genetics Arc is completed by PCs! More information on what that'll include coming up (in the next few days). Those missions themselves will partly be suggestions from the AI based on what questions have been posed on network, just like all three arcs that had been put to vote were player submissions and seen discussed at various lengths ICly on network and throughout different areas of the game.