Agent Bishop has Stockman work on a cure for the outbreak, but he has no successful results. Just then, Bishop is contacted by a mysterious entity offering him an artifact that will help him to protect the Earth. He agrees to retrieve it.
Meanwhile, the Turtles have decided to go to Bishop to find a cure for Donatello.
This episode provides examples of:
- Actually Pretty Funny: Bishop seems lightly amused when Mikey suggests that he has a UFO watching them from space.
- Area 51: Bishop's base is confirmed to be located here by Leatherhead.
- As You Know: Stockman spells out what the characters already know regarding Donnie's cells breaking down, in a Justified example since he's so arrogant he felt the need to confirm what he was already told.
- Behemoth Battle: Huge, mutant alligator Leatherhead is forced to battle huge, double mutated Donnie through Area 51.
- Blatant Lies: When Leo asks if Bishop has a cure, the latter looks to Stockman who is behind the family. Stockman shakes his head, but Bishop lies that he does have a cure anyway to get the Turtles in his employ.
- Book Ends: In "Aliens Among Us", Bishop corners Don and tries to shoot him with a gauntlet-mounted gun. Here, he tries the exact same thing when Don, who's been mutated for a second time, starts tearing up Area 51. Fitting, considering "Aliens Among Us" sets up the Outbreak arc, and "Good Genes Part 1" is the first part of the resolution.
- Character Development: Raph repeatedly objects to cooperating with Bishop, but in contrast to the City at War arc two seasons earlier when he fought Leo bitterly about working with Karai and even briefly walked away, he is far calmer about his objections this time and still goes along with the plan. Justified in that this time, he's aware that Donnie is running out of time and they don't have any better options, but it still shows better control over his temper than he used to have.
- Chekhov's Gun: Stockman's helicopter from "Insane in the Membrane".
- The Comically Serious: Bishop is amused when Mikey suggests he has a UFO watching Area 51 from space, but then quickly snaps back into villain mode as he sharply tells the Turtles how he found them.
- Continuity Nod:
- When the entity mentions "little green men", Bishop corrects him, "little GRAY men", the kind of aliens that were shown to have abducted him in flashbacks.
- Leatherhead mentions his imprisonment and torture at the hands of Bishop that happened offscreen between Seasons 2 and 3.
- This episode emphasizes that Donnie is a very critical part of the Turtles' family and war machine. Without their resident genius, the group can do practically nothing for his condition even with the similarly genius Leatherhead staying with them for the time being. In "Same As It Never Was", Donnie was told by his Bad Future brothers that the family fell apart without him to hold them together.
- The Turtles, Splinter, and Leatherhead pilot the helicopter that they came into possession of during "Insane in the Membrane".
- Deal with the Devil: Leo even referred to making a Deal with Bishop as this.
- Death Seeker: When the Turtles see Stockman is still alive, he says that he too wished that he were.Raph: Stockman? Still alive? I thought we were done with you for good!
Stockman: Oh, I wish. But Agent Bishop didn't see fit to let me rest in peace. - Enemy Mine: The Turtles team up with Bishop and Stockman to help Don and stop the outbreak mutagen.
- Fantastic Racism: The Mystics call Ch'rell an "Utrom abomination" despite previously voicing some appreciation that he showed them respect.
- Find the Cure!: The Turtles desperately need a cure for Don's secondary mutation, fast, as Leatherhead explains that Bishop's alien chemical agent is reacting violently with the Utrom mutagen already in his system, killing him.
- Foreshadowing: A Wham Line from the Foot Mystics reveals that someone else was the Shredder before Ch'rell and that the Mystics are loyal to him, which drives the entire next season's plot. Karai also alludes to ancient powers the Mystics have apparently mentioned before.Mystic: You are nothing but a pretender, like the Utrom abomination before you!
- Godzilla Threshold: Leo briefly considers making a deal with Bishop, but Leatherhead advices against it, having suffered at the hands of Bishop earlier. Then Monster Don ends up attacking Mike when he tries to bring him some food. This makes Leo decide that he will have to make a deal with Bishop, if it means Don can be saved.Michelangelo: I just... wanted to give him some food.
Leonardo: That settles it. We're going after Bishop. We'll make him help Don. - Hesitation Equals Dishonesty: Even after Stockman confirms that he doesn't have a cure, Bishop hesitates before telling the Turtles, Splinter and Leatherhead that he has a cure for Don.
- "I Know You're in There Somewhere" Fight: Splinter to Mutant Donatello two times. One is barely successful, while the other is a failure.
- Internal Reveal: The Turtles find out that Stockman is still alive, thanks to Bishop. Not that Stockman appreciates Bishop's "act of kindness".
- Leg Cling: Monster Don, to Mikey.
- No Good Deed Goes Unpunished: Michelangelo tries to bring some food for his poor suffering brother. Monster Don thanks him by attacking him. This is ultimately what makes Leo decides they will have to work with Bishop.
- Never My Fault:
- When Leo rightfully calls Bishop out for causing the outbreak, Bishop awkwardly says he's familiar with the situation in New York, unwilling to admit responsibility. He also refers to the faux alien invasion as one of his operations in a similar manner.
- Even when he rips into Stockman for the potentially unnecessary transfer of Don that resulted in his escape, Bishop still acts like it's Don's fault that he's on the loose and chides the Turtles for supposedly being unable to do business with him.
- Outside-Context Villain: The mysterious entity is a hitherto unheard and unseen character who has decided to help Bishop for unknown reasons.
- People Jars: Monster Don and the mutant city worker from "Outbreak" are held in these.
- "The Reason You Suck" Speech: With the next episode in hindsight, it's easy to interpret the entity's speech to Bishop as this. He chides him for futilely trying to scrounge for scraps of alien technology and suggests that he will never truly be able to fend off an alien invasion.
- Too Dumb to Live: Just when Monster Don has finally calmed down in the containment cell, Mikey decides that it would be a good idea to open a compartment of the cell to slip his feral brother some juice and cereal. This results in the Leg Cling above, and it takes nothing less than Raph and Leo pulling on them while Leatherhead tries to sedate Donnie and Splinter giving an I Know You're In There speech to pry them apart. That said, all Mikey wanted was to feed his poor brother and he nearly loses a leg as payback.
