The Quarian Ark was an inside job

Who builds five arks when you only have four harbours for the arks? Clearly someone knew the Quarians wouldn't make it, and who doesn't like the Quarians? That's right! - Everyone The Geth! The logical conclusion therefore is that the Benefactor is Legion.

When Jien Garson through seconds of intense research realised that there was only 4 docks for 5 arks, it had no choice but to remove her and her incredible counting ability from the equation.  

As you can see here, the murderer was unarmed, what else do we know that fights unarmed? That's right - Husks! And who do we know that fights alongside Husks? That's right - The Geth! 

Legion did 2818

Javik was right. Should have thrown it out the airlock.