First time the True Shredder (the Shredder that came before Chrell and Karai) is mentioned
It is revealed in this episode that Bishop's first name is John.
Casey and Leatherhead return in this episode after being gone from the show for quite a while.
Mikey: I'm going to call you Zog. Maybe your Zog's great great great great great great grandpappy.
He is refering to Zog the Triceraton from the two part episode Rogue in the House
The Utroms after all the centuries they resides in Toyko, they fled to New York and establish TCRI building, due to Mashimi showed the Foot where to find the the Utroms hideout were.
At the end, Ancient One had a conversation with the shadow characters that looks just like Shredder. Which will reveal the fourth season finale ep., The Ninja Tribunal.
In Stockman's first flashback, his mother comes home and closes the door. Later, when she gives Stockman a chemistry kit, the door is open.
Why, in the first scene, is April in Stockman's underground mouser lab? She didn't know about it back then in 'Attack of the Mousers'!
On the new battle shell, the side says 'Since 1984'. 1984 was when the turtles first arrived in comic books. The title, Tortuga Brothers, translates to Turtle Brothers.
The family photo in "April's Artifact" includes Uncle Augie, but not April's sister Robin.
When Donatello translates the symbols on April's computer, it lists Augie as Professor August O'Neil in the translation
In the beginning before the opening sequence, April tells how her Uncle Augie made her love science, and how he is the reason she got a college degree in math.
April O'Neil has a sister named Robin O'Neil who lives on the West Coast.
Donatello is cut by one of the insect mutants, which affects more than one of the episodes for the rest of the season.
Leo has managed to learn the trick of removing his coat, which had his katana on the outside of the coat, without taking off the swords first; just all of a sudden he doesn't have his coat on, but he still has his swords on.
The special walking stick Leo brought for Splinter sometimes appears on his back, between his katana, but will then disappear in the next shot, sometimes even in the same scene. Then, when he finally gives the stick to Splinter, he pulls it out of a duffle bag.
In the episode, "Same As It Never Was" (series 3), Shredder referred to Donatello as "The Prodical Son" having returned after a long absence.
Leonardo is near some prints in the sand. If they were made by Donatello, he would have to have been walking on his hands, since he only has 2 toes, while the tracks have a 3rd digit.
TMNT Image comics had a female Shredder whose identity was unknown, and it was revealed to be Karai. However, the comic was cancelled before they could reveal the identity of the female Shredder.
The Battle Shell, Shell Sub, and Turtle Tunneler are all destoyed in this episode.