The episode opens in Professor Algernon's lab, and J.T. Marsh is with Algernon as he marvels about the DNA structure of the Neo lords. Algernon says that there are hundreds of different strands from as many different sources, and there are even some that are artificial. As Algernon is wondering how the scientists even accomplished what they did, Marsh asks if he can find any weakness in the genetic makeup that will help them to defeat the Neo lords. Algernon replies, "Commander, I may be the most brilliant physicist in the entire solar system, but I'm no biologist. To break the Neo lord's genetic code, and find some kind of weakness, we'll need the most brilliant geneticist in the solar system, or at least the most brilliant Terran geneticist." The monitor on the wall then rotates between pictures of Neo sapiens, but finally a Terran is shown. It is a picture of Albrecht Ketzer.
Marsh is next seen landing on Venus, at the Burns farm where Nara is at the gravesite of her parents and brother. See is planting a sapling at the foot of the graves, and is on the verge of tears as she speaks of how it will be nice when the tree grows. Marsh tells her that Marsala and he are going on a mission, and they need one more volunteer. She agrees to go, saying, "There's nothing left for me here."
In Earth orbit a pirate ship decloaks, and the three e-frames of Marsh, Burns, and Marsala exit. In the area of the Peruvian Andes Marsh explains that because Neo sensor coverage at that end of the Amazon is minimal they should be fine as long as they stay low and follow the river. Nara asks why a scientist would be in such a secluded place, and Marsh tells her that Ketzer went there ten years before the war began to study the use of rare plants in gene therapy. Marsala notes that his theories were far in advance of even Neo sapien science. Marsh goes on to say that there has been no contact with him since the war began, when he was cut off.
As the three round a bend in the river they suddenly face three Neo e-frames, which immediately open fire. The exotroopers scatter, Marsala cloaking. When two of the Neos go after Nara, Marsala uncloaks behind them and destroys one. Nara turns the tables on the other and chases it a short while before destroying it. Marsh uses his superior piloting skill to cause the Neo trailing him to crash.
There is an old seafaring ship near the docks at Manaus, Brazil; it is apparently the command station for area Neo activity. Draconis is attempting to contact one of his reconnaissance parties. When he wonders why they don't respond, Medusa suggests, "Our patrol reported three Terran e-frames before losing contact. Perhaps they are no longer able to respond." Draconis then orders all their e-frames to converge on the intruders and destroy them. When Medusa tells him that they are no longer on their sensor screens he tells her than in that case they should begin a search from their last known location. She goes to relay the order.
A group of Neo frames fly over the river, and once they pass the exotroopers resurface. They proceed without exiting the river in the hopes of avoiding detection. Nara asks how they'll find Ketzer if they're grounded, and Marsh tells her that Ketzer's old research station is just a few miles off. As they proceed a pair of eyes watch them from the jungle.
On the deck of the Neo command ship Draconis wonders what the ExoFleet could want in the insect-infested jungle. When Medusa says Ketzer, and speaks of his failures to capture him, Draconis is still perplexed. Draconis says that he was a failure, and his theories were dismissed and ridiculed by reputable Neo sapien scientists. Medusa observes, "Yes, we often ridicule what we cannot understand. An expert in genetics would be a great asset to the ExoFleet, and a danger to us." She says that Phaeton would reward whoever was able to capture Ketzer. Draconis complains about his assignment, and states that he is a clone and should not be punished for what a previous Draconis did wrong. She tells him, "One might mistake you for the original Draconis."
The exotroopers are now flying a few feet above the river. Marsh says that Ketzer's clinic was in a village just ahead, and if he isn't there it'll be a good place to start their search. Suddenly they come under attack, being fired at from the jungle. They return fire, but soon a boulder on a rope swings to knock Marsala off course, and a net fall to trap Marsh and Burns. Nara gets them free, but she, and soon the others, start getting pelted by sacks filled with a white liquid that covers their windshields and obstructs their view. A buzzing sound can be heard in the forest. Marsh orders them to get above the trees, but Nara is hit be a rocket before she can escape. She crash lands, exits her e-frame, and fires a few shots into the jungle. A person whose skin is entirely green shoots a blowdart that strikes Nara in the neck, bringing her to her knees. She is approached from behind, and when she turns she screams upon seeing a man with entirely green skin, what looks like moss for hair and has roots growing out of various parts of his body.
Marsh and Marsala hear her screams, and go to get her. She and her e-frame are already gone, but Marsala notices one of the attackers fleeing. They pursue him into a large pond when they are suddenly attacked from all directions. Marsh orders Marsala down, and once he does Marsh fires his Solar Flare, which evaporates all the water in the pond and devastates the nearby vegetation. All the attackers now appear to have left, and Marsh figures that they were not only lead into the trap but also away from Nara. He wonders where they've taken her, and Marsala states, "The more troubling question is, why?"
Nara, unconscious and inside a net attached to a pole, is being carried by two of the green humans along a path up a mountain with a waterfall. Behind are another four carrying her e-frame. A village can be seen on the summit. They arrive at daybreak, and Ketzer watches from the shadows as she is set down.
Later Nara awakens on a bed, her right arm in pain. Ketzer enters, saying, "Do you know what life is? Life is a river, a dark river that flows inside us, changes us. Then, in the end, it drowns us so new life will form." "Doctor Ketzer?" Nara asks after a pause, with some disbelief and shock. Ketzer has splotches of green on his forehead, and along a muscular physique. His left hand is green, and somewhat different. He replies, "Once I was Ketzer, now I am... something more." She almost falls as she tries to get to her feet, saying as she does, "I'm... Lieutenant Burns of the ExoFleet. We... we need your help if we're going to beat the Neo sapiens." With anger he shouts, "You don't have the courage to defeat the Neo sapiens! Are you willing to destroy yourself?" She seems somewhat confused as she starts, "I... I'm a soldier, every time I go on a mission..." and Ketzer interrupts, "I'm not asking if you would give up your life. Would you sacrifice yourself, what you are, for what you could become?" "I.. I don't understand." He chuckles and tells her, "You will."
Marsh and Marsala are flying in a crisscross pattern over the river. As it seems fruitless, Ketzer contacts them on Burns'frequency, something Marsh notes with anger. Ketzer says he will explain, and that he will leave the signal open so they can home in on it. Marsh tells him not to, since the Neos could also home in on it. Ketzer then tells him to go to village on the escarpment near the waterfall.
Back at the Neo base, Medusa reports that a transmission from the area of the headwaters of the Rio Negro was noticed by one of their patrols, but because it was so short the exact location couldn't be pinpointed. Draconis gives orders all patrols to the area to find the source. Medusa suggests that perhaps the commander should personally lead the next phase to ensure success and reap the rewards. Draconis likes the idea that Phaeton will have to give him what he deserves, and he orders his e-frame prepared as he boasts that he will destroy the intruders and return with Ketzer. Once he leaves Medusa contacts Livia. She reports that Livia's suspicions were correct, the current Draconis only serves Phaeton to advance himself. Livia says she will have him replaced, and when Medusa doubts he will give up what little power he has, Livia states with a smile that a squad of Neo lords should change his mind.
Meanwhile Marsh and Marsala arrive at the village. Ketzer comes out to meet them, and Marsh wonders if it is really him. Ketzer explains that DNA from plants and animals is attached to a retrovirus and injected into a human. The virus penetrates the cells, and as the renew themselves the body grows in a new manner. Marsala says that gene therapy was meant to cure diseases, not remold humans, and Marsh agrees, saying that he is acting against the laws of nature. Ketzer is angered, and states that he is the law in this place, where civilization has no meaning. He states that beforehand the indigenous people were outsiders, but now they are truly a part of the jungle, it flows through their veins.
Marsh is growing angry. He asks where Nara is, and what was done to her. Ketzer has her brought out and says she is in no danger. Marsh tells him that she needs a real doctor, and that they have orders to take him back as well. Ketzer expresses his firm belief that he belongs where he is. He asks the exotroopers to use their e-frames to launch an attack on Manaus. Marsh says no, that there are still Terrans in Manaus and there would certainly be Neo retaliation. Ketzer turns to Nara, and asks if her arm hurt when she awoke. She says yes, and he explains, "I injected her with the same DNA formula I use on myself." Marsh approaches angrily, "You're insane!" Marsala tries to calm him, saying, "No J.T.! We need him now, more than ever." Ketzer says, "There is a compound that would kill the virus before her DNA is permanently altered, but only I know what it is. You will help me destroy the city or watch your Lieutenant Burns slowly become what I am."
Burns frees herself from the grip of the green men on either side of her. She approaches Ketzer and speaks of how he came there to help people. He responds it is the native who want Manaus destroyed, and that it is a knife in the heart of the jungle and is very out of place. He says that only their weakness prevented them from destroying it, but now he has made them strong. Nara says, "You've turned them into freaks, robbed them of their humanity." He responds, "I've helped them to adapt, to improve. You find us ugly because we don't look like you, we'll see how your opinion changes when you're one of us."
Marsh concedes. He says they will help Ketzer destroy the city, drive out the Neos, and relocate the Terrans. He sets one condition, that Ketzer give Nara the compound to prevent the mutation immediately. Ketzer agrees, and says it is in his hut. Just then the building he is pointing to explodes, and Neo e-frames swoop in attacking. Marsala and Marsh return fire, and village residents scatter. On Marsh's order Marsala takes off. Burns runs for her e-frame and enters. Ketzer tells his people to fight them since they do not belong in the forest, and the villagers do. At least one has gotten to their armory and begins to open fire. Marsala takes out a Neo e-frame that is firing on the village. Villagers succeed in causing a Neo frame to crash by blinding it with the same white substance used earlier. Other Neo frames have success fighting the natives. Marsh takes out another Neo frame firing on the village, and orders everyone to take to the forest. Nara fights off a few others, destroying one. Marsh realizes there are too many, and orders Marsala to pick up Ketzer. Marsala uses his weapons to stun Ketzer, who with villagers is firing on the Neos, and the villagers nearby scatter. He lands to pick Ketzer up and deposit him in the rear seat of his e-frame. He takes off and the exotroopers flee.
Draconis orders pursuit, and the Neos do. Nara doesn't want to abandon the villagers, but Marsala says that without Ketzer they will likely retreat into the forest and the Neos will be unable to find them. The Neos are firing at them, and so the go below the tree line. Marsh has Marsala go to stealth mode as the Neos follow them into the forest. Nara gets behind two Neos and destroys them. Marsh simply maneuvers through the trees until his pursuer crashes into some. Draconis is in disbelief that they might be defeated by only a couple of e-frames. He tells his troops to pursue and that he will return with enough firepower to have the entire forest leveled, and he leaves. Nara doesn't want to let him escape, but Marsh figures Ketzer is too important to risk.
Above the trees Draconis sees six e-frames approaching. He is pleased until he realizes they aren't from his unit, but that they are Neo lords. They encircle him, the leader saying, "Your services are no longer required, Draconis. You are relieved of your command." The point their weapons at him as he screams, "Noooo!!!!" Below the exotroopers see a giant flash above the trees, and debris rains down. Marsh goes up to see what happens, and sees e-frames departing. "I don't think there's going to be anyone following us now, " says Marsh.
The three land, and all four exit. Marsh tells Ketzer he won't have any more problems with the Neos, and asks what they can do to get Nara the antidote. Ketzer tells them that there is no antidote, and that he was lying earlier. He says that once the injection is given the mutation is inevitable. Nara is in disbelief, and is worried about what will happen to her. Marsala tells her, "What is inside a person determines true beauty, outside appearances do not matter." She raises her head out of her hands to respond, "They matter to me!" Marsala seems disappointed, "Yes, of course they do. How could it be otherwise?" Marsh angrily tells Ketzer, "Alright Ketzer, get in Marsala's frame. If you can splice genes, you can unsplice 'em." Ketzer says, "I am part of the rain forest. I'll never leave it alive, and neither will you if you try to force me." Noises are heard from the surrounding trees, and the exotroopers turn to face possible attackers. Marsh says, "Call 'em off, Ketzer." When he turns back, Ketzer is gone and he calls out Ketzer's name to no avail.