On the plane, Albert showed a picture with bad Cooper's house in Rio, obviously he's lived there for a while since the dark tan on his face. He then teamed up with whoever made Phillip Jeffries disappeared in Buenos Aires, Rio is relatively not that far from Buenos Aires.  

The one that made Phillip Jeffries disappeared is the leading figure of Blue Rose aka the "MOM" who was banging the door, and is much more powerful, possible from outer space and can create double or more doppelgangers, also responsible for Major Graland Briggs's head floating in space.

This alien and bad Cooper had set up the argent lady and Ike the Spike, also controls Todd, to prevent Bad Cooper going back to the lodge, no idea who set up the glass box in NYC.

It will be Alien power+black lodge+bad Cooper VS. good Cooper+FBI+Humanity, hard to predict who will win.....