When the feds smelled anti-competitive behavior on Apple’s breath in July after the computer maker rejected an iPhone app for Google’s Voice calling service, the FCC asked Apple, its telecom partner AT&T and Google to explain what happened.

When the three tech giants replied three weeks later, one decided to file part of its answer in secret.

Oddly, that was Google — the ostensible victim in the incident and a company that prides itself on its openness and transparency.

Google’s decision (.pdf) causes a big blind spot in the story of the highest-profile mobile app store rejection yet — a story that is likely to change how app stores are run, how people expect apps stores to be curated, and whether the feds decide to regulate them.