This is also the first time Xever appears without Shredder or Bradford.
Aesop Amnesia: In The Gauntlet the turtles learn that being overconfident can be dangerous, but they seem to have forgotten that lesson when they met Xever as Fishface, which comes back to (literally) bite Raph in the shell.
"What has two robotic legs and loves to stomp on Turtles? THIS guy! Heh heh heh heh!"
Call Back: Two specific call backs to "It Came From the Depths"; the Shellraiser is made from the old subway car Leatherhead was living in, and the Turtles still have the Kraang power cell he gave them.
Also, Pulverizer's flashback depicts the turtles fighting Stockman in "I Think His Name Is Baxter Stockman".
When the Turtles are wondering who would be interested in stolen alien technology. Leo, Raph, and Donnie say "Baxter Stockman" in unison, but Mikey says "Donatello". This is a reference to how Donnie created his robot in "Metalhead".
First time a Kraang-droid has appeared wearing the businessman disguise since "Turtle Temper".
Freeze-Frame Bonus: When Donatello hears the news about Raphael being poisoned, he takes a makeshift medical kit which, in marker, has the words "Donnie's Box" on it. Under that is another sentence, also in marker, saying "MIKEY, DO NOT TOUCH!".
Hope Spot: It looks like Pulverizer will make himself useful when he goes for the leg take down to try and stop The Kraang from taking the Power Cell. However he's unable to fully execute it and gets batted aside.
It's All My Fault: The Pulverizer feels this way when Don has to rescue him, losing the chance to get the power cell back from the Kraang. Don pins some of the blame on himself, since his (justified) reckless driving broke the lead shield protecting the power cell, allowing the Kraang to track it.
Shown Their Work: When Mikey tells Donnie that Raph was bitten by "a giant poisonous robotic fish", Donnie corrects him saying that it would be venom, not poison. Yes, there is a major difference between poisonous and venomous, and they're not interchangeable.