Secrets are hidden rooms with a "secret" crate inside that contains valuable goods such as energy, health packs, and weapons (and not the small kinds like cat food or health pills, we're talking about canned beans and full health packs).
Secret rooms are often at the back of offices with a transparent ? on it. Be sure to check at the back of every office you happen to come across to! Most of the time, quests will lead you to offices with secret rooms. (Or, you know, just check out this page for their locations.)
You can find out how many secret rooms in one episode by checking the episode progression, which would have 0/# of secrets in the episode that you're playing in.
|Episode 1||NO SECRETS|
|Episode 2||Back of the room with the fuel.|
|Episode 3||12 East Street / Office Level 3 / Bathroom|
|Episode 4||9 East Street / Level 2 / Bathroom|
|Episode 5||7 Grove Street / Level 3 / Bathroom|
|Episode 6||2 Rando Street / Level 3 / Bathroom|
|Episode 7||9 Blake Street / Level 2 / Bathroom|
|Episode 8||12th Street / 2nd Floor / Bathroom|
|Episode 9||12 Demamp Street / 2nd Floor / Bathroom|
|Episode 10||10 Turner Street/ Level 2 / Bathroom|