The story is mainly told as if the reader is reading stolen documents detailing the Powerpuff Girls' lives. The story chronicles them, starting prior to their creation in the 1980s. Project Powerpuff: Declassified adds a more "realistic" science-fiction element to the franchise and rolls with it.
The second story in the series is The Powerpuff Girls: Declassified.
This fanfic provides examples of:
- Adaptation Name Change: The Professor's real name is "Thomas Lewis Upton". "Utonium" is a code name.
- Alternate Universe Fic: Project Powerpuff: Declassified's summary calls it a "gritty and mostly realistic re-imagining of The Powerpuff Girls".
- Dark Fic: Most of the charm and fluff of the original has been replaced with dark sci-fi drama.
- Doorstopper: The first story totals at over 130 chapters and almost 500k words. The second one is over 200k and ongoing as of August 2019.
- R-Rated Opening: The prologue starts with a violent fight between Blossom and Ace, setting the tone for the story.