The online community for bionicle has done a solid job of archiving and even polishing the various content that was released over the years. There's a site that collected all of the flash games [0], and someone stitched together a few versions of the "Biological Chronicle" [1], which is every book, comic, and even transcriptions of two of the flash games that had an actual narrative, woven so the narratives all line up.

[0] https://biomediaproject.com/bmp/ [1] I don't have a link handy to the ebook, I'm also not sure if they had permission to upload all of that content in one file or not