That looked like a silhouette of her brother, so her brother was the one who cause the original knight to go berserk? and I'm pretty sure he is the mole the gorilla was talking about.
Guy talking shit about his sister.
Purposely making chaos when he's suppose to be protecting.
The brother is bat shit crazy.
I mean, the manga give us at least 3 reasons why he would shoot him.
From Beta just happens to be the right size to fit all the fetish outfit they came across in some random guy's house to Cid just happens to be the same age now as he left Japan in his previous life so he can still fit in his old uniform.
If I had to guess, the brother isn't really her brother, he must have changed her memory or something like this, and the one who knew about it was killed to shut him up just before the fake brother did his experiment. He must have chosen "her" sister before Beta showed up.