[1] The transport modules from season 3 are reused, this time to drill underneath Canada and into New York City.
Michaelangelo's strange dreams lead him to seek out Mondo Gecko, a lizard who was caught in the same ooze as the Turtles.
When the city is hit with a sudden termite infestation, the only superhero who can help—Bugman—is too at peace with himself to aid the Turtles in defeating it.
A malfunction of Donatello's latest invention ultimately results in Raphael believing he is about to die, and ultimately trying to save the world by himself Baxter Stockman leads a swarm of flies in an attempt to conquer New York and prove his worth to Shredder and Krang so he can become human again.
Title Reference: Lord of the Flies Note: Like in the fourth season in the series Son of Return of the Fly II Bebop and Rocksteady botch another mutagen experiment, resulting in a giant ice creature who Bebop dubs "Frosty", and Shredder uses this monster to freeze New York solid, preoccupying the Turtles long enough for him to steal thermal explosives needed to melt the Technodrome free from the ice.