I don't think their intentions are clear. It's more that a powerful organisation or government now has control of it and is planning something large scale, beyond what we'd seen in the film before.
It isn't explained, which is my main fault with Primer. Primer leads you in with a crystal clear beginning that makes sense, but goes off the rails by the 2nd half.
A lot of people are tricked by the crystal clear beginning and assume that the end makes sense, but the movie goes into ambiguous mode about half-way through. Its audience interpretation, as opposed to a singular answer. (Contrast with something like Inception, which doesn't really have more than one interpretation).
Some people like ambiguous movies. I don't, which is why I kind of prefer Stein's Gate, where all actions are clear.
---------
Either way, its clear that the powerful organization is Aaron's goons. Aaron was the guy who played the stock market with the time machine, so its obvious that Aaron used the time-machine for ill-gotten gains at that point... and is using the money to fund a bigger time machine.
