Bite into a Thomas’ English muffin and, it turns out, you are about to swallow one of the most closely guarded secrets in the world of baking.

The company that owns the Thomas’ brand says that only seven people know how the muffins get their trademark tracery of air pockets  marketed as nooks and crannies  and it has gone to court to keep a tight lid on the secret.

That leaves one of the seven, Chris Botticella, out of a job  and at the center of a corporate spectacle involving top-secret recipe files, allegations of clandestine computer downloads and an extreme claim of culinary disloyalty: dumping English muffins for Twinkies and Ho Hos.

Mr. Botticella, 56, delved into the mystery of Thomas’ muffinhood (hint: it has nothing to do with the fork), after Bimbo Bakeries USA bought the brand early last year. At the time, Mr. Botticella was a Bimbo vice president in charge of bakery operations in California.