Yeah the fights scene at the end was pretty cool.
My guess since the big bad appears to be the Mom's boss that they actually created it and the junk was on the plane, then it got in the water after the crash.
I'm pretty sure the Partner was dead, as for shooting the guy in the back....
He only broke the roof the first time he did it, after that he seemed to have better control over it. As for why no noticed him jumping, well how often do you look on top of roofs while you are on the ground?