There are two secret squirrel locations, as well as a secret area for the achievement "Detour."
1. Before you enter the "Secret Base," there is a crudely made nuclear warning sign on top of the entrance of the base. If you jump from the bike towards the sign, the player will get caught in a slight forceful wind, carrying the player up to an area that will reveal several squirrels sitting on a staircase behind a fence.
2. Once inside the base, a ways down, there is a wall compartment that will slide vertically shut. Without reverting to the checkpoint closest to the moving wall, you won't get a great look, but reverting to the checkpoint will reveal a squirrel sitting on a missile before the wall closes entirely.
3. And now for the Achievement room (spoiler alert). After breaking through the glass at the 5th checkpoint, drop down to the lower platform with the no bikes sign rather than jumping the railing to the stairs. Once there, reverse into the beware squirrels sign and the other sign will fall. Jump out the newfound gap and over the fans into a checkpoint underground. Carefully maneuver your way through the rings of fire forward, up, and backward and budink! Achievement unlocked.
This section is reserved for Confirmation/comments about this investigation. Investigations will remain open until advised by Redlynx that the final solution for each secret is found.