Hi there... welcome...
Aye... your questionary is really newbie 100% XD
1. Safeguards... it is explained later, when Musubi gets xxx (no,not porn
). If you look at blade, you can see SG (safeguard) logo on it... About how she get it - "life goes in mysterius ways" ... 
I personaly like the way - she picked something in store as cold weapon - in case smg is not enough - and it turns out to be something like that - LoL
2. 7th chp is extra story called Negative Corridor - if you take a look around, you can find thread...
3. No, that was originaly the order - trying to get chaos from Netsphere, they found the way to download SG in victim. So they grabbed Clawsa when he was investigating with Musubi, and then when she found them - they activated download... Now logical point is that if whole City is controled by Netsphere which is governed by Governing Agency (GA) and protected by SG - forced download of SG, erased Clawsa, but he was able to transfer him self to Netsphere in order to survive...
Btw, there is thread for Noise, so please take a look, to maybe find some answers you are looking....
Have fun here