how did she become a weapon??

What a coincidence...right after Saikano I was about to watch Serial Experiments: Lain because I heard it was a mind**** and that it was pretty good. "The Melancholy of Haruhi Suzumiya" is also a pretty good series about existence/reality but it wouldn't really go on top of my favorites

Anyway how I think Chise became a weapon is that they needed and edge in the war and somehow she happened to come to know about them taking guinea pigs for experiments or something, and she wanted to become stronger because she was always feeble as a kid so she volunteered except she didn't know the consequences but eventually accepted them.

Another plausible idea is that she was created because the old guy who always wipes his forehead says that Chise is created from the same components as a human is made up of or something very similar to that line in the 10th episode where he tells that to Shuji because she needs those medication pill things. I think there might have been some sort of mistake/accident and Chise didn't come out as the result her creators expected because the guy keeps saying it's nobody's fault that she's this way. They probably intended for her to be some sort of perfect weapon but there were some flaws and she became too human-like as a prototype or whatever

But there seems to be two parts of her struggling subconciously for control; a human part and a machine part. You can see this towards the end of episode 11 where they have dramatically different thoughts speaking to Shuji, like the Chise human part asking him to help her and the machine part wanting to kill him. You can also see sometime during the series where she says something with a blank facial expression, then she reverts back to her human personality and she has no idea what's going on

Or it could be something else