I've just finished watching it for 2nd time, and I've been wondering about the same thing, what was the motive.
Truxton - I think his motivation is the same as the rest of Atlas McDowell, they are all in their 60s from vietnam war, cold war era. Although they have been blatantly earning money on world disasters thanks to API, in their minds they're probably also thinking that they are protecting American interests in everything from economy to nation.
Kale - I think his ambition is to take over API, legally.
Kale and Maggie - Kale isn't dependent on Maggie, he "owns" her, he brought her in to do his dirty job, it just so happens he's a kind enough to solve her issues. But I assume he's doing that so that she can stay focused on her tasks.
Tom - probably got sick of killing people and "fake excuses" for doing so.
Illuminati/Atlas McDowell - I am guessing they must have been really scared of what Will knew or whom he's passed on the information. I don't know why they didn't just try to kill him as well as they did Katherine... I guess he was just lucky that they decided to sever ties with Truxton instead.
Andy - it's hard to say. She could be either Tom's mistress, daughter, a friend or an employee. That could be one reason why she was at the apartment.
Another reason could be that she worked for AM and that they knew about the place and sent her there to snoop, queue in Katherine.
Unfortunately it was not explained, so she could be anybody.
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Fresh Prince Of Bel-Air
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