The Case Files are PRT designation for investigations it has conducted. The number comes from sequential investigations with each files being an investigation that was started chronologically after the previous one.
If it has to do with parahumans the PRT will look into it until the situation is resolved. Consequently the PRT and it's ancillary organization handle a wide range of material in the persuit of safeguarding the public good.
As the PRT post dates the appearance of parahumans many of their files were consolidated from sources collected from other agencies. Thus it included events that already happened. Later recorded cases included:
↑ 1.01.1Official files. Classification documents. Then there were the notes for case one, case fifteen, case thirty-two, case fifty-three, case ninety. The ‘cases’ were the events the PRT had deemed of interest. Riddles both solved and unsolved. My collection there was incomplete, but some were official enough to be confidential, and I’d never had that access. Others were closed, the mystery deemed nonexistent or something to be folded into popular knowledge. - Excerpt from Daybreak 1.1
↑ What Alexandria had termed Case fifty-threes, after the fifty third file in a series of unresolved, difficult-to-explain parahuman events, one of the only ones to truly develop in their records. The Doctor had termed them deviants. - Excerpt from Interlude 28
↑ 4.04.14.24.188.8.131.52.7Case zero was Scion. He was also, I presumed, the last case. Case one was the Siberian, technically the one who had first started the case files, as the PRT consolidated old data and tried to get information from other government agencies. Case two was Behemoth, his rise had incited the creation of the PRT. The case series had been an excuse to gather data from international agencies, too. Case three was the lie of the virus, an early claim about the origin of powers, propagated by an early online newsgroup. Case four was The Player, an early Thinker mastermind who had required some greater cooperation across multiple agencies to root out. Later on, The Player would be a case-in-point for the formation of Watchdog and its core purpose. Kenzie’s would-be group.
The first cases had inspired things, major functions and interests. Committees had been formed and those committees had become something. Even though a whole chunk of the early ones were minor or fabrications in the end, the virus theory included, they’d led to things like a dedicated parahuman science department. - Excerpt from Shadow 5.10
“I can’t tell you how bummed I am that it isn’t case sixty-nine instead, but no, that number went to a bigfoot sighting or something stupid. A stupid bit of immature humor would’ve been the one good thing in this mess of a thing.” - Excerpt from Flare 2.6
↑ 9.09.1All the talk of cases. Case Twelve. I turned to the Old Man. I’d thought of him in the same way I thought of sinister and ominous things in the background, like the Slaughterhouse Nine. The Nine had even been a series of cases, with Siberian’s attack on the Triumvirate as case one. - Excerpt from Black 13.8