At the beginning of "Rise of the Turtles, Part 2", Mikey wants to drink some mutagen, but Donnie points out that it may turn him into a pile of goo. Fast forward to "The Pulverizer Returns"....
It's also a fast forward to "Mikey Gets Shellacne" where we see what happens when Mikey does use more mutagen on himself.
Any moment between Raphael and his pet turtle Spike becomes this after Spike mutates into Slash.
Any moment that Irma is on-screen becomes this after the reveal that Irma is a Kraang in disguise who became April's friend in order to get April to lead her to the Turtles. You can see how everything this character says is a subtle manipulation to earn April's trust in her and sometimes erode April's trust in others, such as Casey. Every little quirk is a foreshadowing of what this character really is, such as her encyclopedic knowledge of the behaviors of rats, an innocent enough interest for a Perky Goth but also something valuable when tracking Master Splinter. Or the gluten-free diet a Kraangdroid mentions in passing when Irma is the only prominent "human" character to stick to the same diet.
In "Alien Agenda", Karai is fascinated by the mutagen since that's where the "monsters" come from. Raph tells her to "lean in for a closer look", which is harsher because of what happens in "Vengeance is Mine".
In "The Fourfold Trap", Karai tricks the Turtles and April into thinking the Kraang are back and that's exactly what happened in "Annihilation: Earth!".
In "Enemy of My Enemy", Karai states that Shredder's vendetta "is going to take us all down". As of "Annihilation: Earth!", Shredder really has taken down everyone.
In "Mutant Gangland", Splinter tells the Turtles that someday he won't be around anymore to remind them of their foibles. This is just a G-Rated way of saying he'll die eventually and the Turtles will have to live without him. By "Requiem", let's just say that "someday" came sooner than expected.
Given that "Tale of the Yokai" featured the Turtles realizing that the events in the episode and their part in it were always fated to happen, chief among them Tang Shen's death. While the Turtles buy Splinter some time in "Earth's Last Stand", "Requiem" shows him dying the same way he did in "Annihilation: Earth", implying that he was always fated to die by the Shredder's hands.
In "Owari", Leo calls Shredder a demon during their final confrontation. In the fifth season, they have to deal with an actual demon (Kavaxas) who apparently makes a deal with Tiger Claw to bring Shredder back to life. Granted, this could just be foreshadowing.
When the Turtles accidentally mutate Kirby into a mutant bat, Mikey wonders if he would bite April and turn her into a vampire. During the Halloween arc, April along with Casey, Raph, and Donnie are turned into vampires.
The "Raphael: Mutant Apocalypse" three-parter has quite a few of these:
The mutagen bomb that changed the world is basically what might've happened had the Turtles failed to disarm the Kraang's mutagen bomb in "The Gauntlet" and also brings to mind the incident when the Turtles accidentally scattered mutagen canisters over New York in "The Mutation Situation".
Slash claims that his antagonist actions prior to his Heel–Face Turn was because of the mutagen and he "wasn't right in the head", the mutagen bomb causes Leo to suffer a second mutation and spends several years if not decades as a fearsome warlord/gang leader. On a meta example, his secondary mutated form resembles Dark Leonardo's physiology from the 2003 series' Fast Forward season.
Throughout the show, Leo and Raph's sibling rivalry was effectively a toned down reflection of Splinter and Shredder's rivalry with Leo as Splinter and Raph as Shredder, who became a crime syndicate leader. However, in this alternate future, Leo is the brother who ends up taking Shredder's path of suffering body horror, leading a gang, and even wearing a mask while Raph simply focuses on surviving with whatever family and resources he has left, much like Splinter in "Lone Rat and Cubs".
For something that was nothing more than an offhand comment by a filler villain, Don Vizioso's fear of mutant apocalypse is now jarringly accurate.
In "The Invasion", Kraang Prime claims he used mutagen on the monkeys which created early humans. The very thing that created the human race is also what ended it.
Donatello downloaded his brain into Metalhead, much like how Professor Honeycutt had his brain transplanted into his robot assistant's body. On a meta example, a Fast Forward episode has the Turtles reading a (fake) journal in the future containing information about events in their lives they hadn't lived yet, Donatello's section contains a story about him becoming a disembodied brain and having to be transferred into the body of Cody's robot butler Sterling.
In the third season, Leonardo briefly distrusts Slash due to the fact that he'd tried to kill him and his family before while Slash somewhat meekly admits fault and he also notes that the Mutagen messed with his head, which is an excuse Leo doesn't buy. In the "Raphael: Mutant Apocalypse" three-parter, the Mutagen Bomb both mutated Leonardo and put him in a mutagen-induced rage for decades before he was finally cured of it.
