[mikegagnon]

In the American justice system the judge is part of the judicial branch and the prosecutor is part of the executive branch.

Prosecutors have a huge amount of discretion in their jobs. They can choose if they press charges and if so what charges to press.

In this case, there are allegations that the prosecution abused its power by retaliating against free speech.

The prosecutor allegedly said something along the lines of: Aaron Swartz was foolish to exercise free speech because it then went "‘from a human one-on-one level to an institutional level.’ The lead prosecutor said that on the institutional level cases are harder to manage both internally and externally"

I presume by "one-on-one" prosecution, the prosecutor meant it was one prosecutor against Aaron Swartz. But by publicizing the case, it aroused the interest of the "institution" (i.e. the higher ups), who then decided to throw the book at Swartz.