So.... Must be Tuesday
#TRUTH
But seriously, Pax's agenda is only hard to see if you're either A) in the thick of things on the ground, or B) don't know of Pax's history or involvement with the situation. She never got the chance to truly tear down a hated foe, her plans to spread the Dissonance through the ashes of the Matrix with Jormungand fell short, and she's a psychotic bitch who would do anything to achieve her goals and has zero qualms about burning the world to get them.
From what I can see, there are three main goals on Pax's agenda:
1) Deus. Pax may have 'killed' him with Jormungand during the Crash, but that's not enough for her. Bullet to the brainpan isn't the slow, torturous dissection she really wants. She wants Deus to suffer. Her 'issues' with other AIs are merely an extension of her hatred of Deus for his betrayal. So she brought Deus back so she can kill him slow, and throw blame on everything that comes later on his head.
2) Dissonance. Pax is a Dissonant technomancer, which is basically the TM version of a Toxic Shaman. Spreading the Dissonance and eliminating anyone and anything that gets in her way is a core part of her insanity, and has been since she was a Fading Otaku, desperately trying to hold on to her powers.
3) Addiction. Pax spent over a year in the UV sections of the SCIRE's host. She is an addict to that hyperstimulation, and so she'll do anything to get access to hosts of that level (which is likely how she ended up working for the megas, anyways). Turning Boston into her dystopian playground, and using her minions to create Dissonance pools may help her take over the hosts of the megas in Boston, especially NeoNET.
Remember, though, that while Pax is a crazy bitch, she isn't the 'talking to flying squirrels' or 'tin foil helmet' kind of crazy. She's Hannibal Lector. Cold, cunning, and dangerous as all hell.