The third season is starting to build up a rather interesting storyline, if I were a guessing man I'd say this is how the plot is going to work, and yes I know they're out of Order:
Riddle of the Sphinx
Following the cliff hanger of the season 2 finale Van Kleiss disappeared, here we learn where he went.
A Brief History of Time
Van Kleiss returns to the present and is recruited by BK into the New Nanite Project using the information from Riddle of the Sphinx.
Yet another Nanite Project scientist found, Peter Meechum.
Black and White
First of the unknown amount of Meta-Nanites are found, history about them is also explained. Cesar begins the process of reviving Gabriel Rylander and restarting the Nanite Project.
Assault on Abysus
Second Meta-nanite is found. All Abysus residents forcibly inducted into Providence's army.
Collars get a upgrade, E.V.O.s can now be controled directly.
Crash and Burn
Potential allies gained in Moss and his crew, and control nanites acquired for use in defense against Providence.
Now allow me explain my theory, Black and the Consortium are trying to use the new nanite project to recreate the Meta's or use them to create a whole mess of E.V.O.s, which are then used in a assault on the Dam Base. Control nanites are then used to fry their collars, and as a side effect gives the E.V.O.s more control over themselves.
Rex then takes his new found E.V.O. army and kicks Providence's butt. I am at lease hoping that Van Kleiss's millenia spanning journey changed him personality wise, hey a guy can hope can't he?