Up until the last three minutes, The Remains of the Platypus is told in reverse order. To later help jog his memory (affected by a Doofenshmirtz contraption), Perry writes a note to himself on his chest.
When the tower retracts the dome and creates a bigger dome, trapping all of Danville inside it, is an allusion to when Springfield was also trapped into a bigger dome by Russ Cargill and the Environmental Protection Agency.