The episode seems to begin in some sort of arena, as we see some spotlights placed among darkness above that shed light below. In the background is heard feral growling and roaring. As the noise continues we are soon shown a hallway ending in a metal door with a circular window that has vertical bars. The spotlights are attached to different part of the ceiling and walls. The view closes on the door, and the window. A blue, four fingered hand is raised into view, and it appears to be Neo sapien hand that is somewhat melted, since there is a liquid quality to it.
Marsala sits with his eyes closed, and his body shakes before he opens his eyes with a shout. J.T. Marsh runs in, asking, "Marsala! What's wrong?!" Marsala is holding his hands at the sides of his head as he shakes his head back and forth. He replies, "I had what a Terran would call a nightmare." Marsh is somewhat surprised, "A nightmare? Neo sapiens don't sleep. You okay?" Marsala turns away from his computer terminal to face J.T. and explains, "We Neo sapiens can make parts of our brains become dormant to rest them. Mental activity sometimes continues, producing what you would call a dream." Marsh says before he turns to leave, "Well, as long as you're all right, I'll go back to bed." As he begins to walk away Marsala asks, "What do you fear most J.T.?" Marsh is surprised by the question, and he turns back to face Marsala again as he responds, "Huh? Well, I guess that I'll make a mistake that'll cost the life of somebody in the squad. What are you afraid of?" Marsala just shakes his head, obviously not wanting to answer. Marsh walks the last few steps to him and says, "Come on, I told you, now you tell me." Marsala tells him, "Let's just say I fear what might happen in the future." "Why?" "Because it's a door we must open with no knowledge of what lies on the other side." With that, Marsala turns back to face his computer terminal, shuts it off, stands up from his chair, and walks away.
At Vesta Space Port on Venus, Draconis and Creon wait as a shuttle arrives. Draconis is complaining, "Either I am in command of Venus, or I am not. I don't like getting orders from Phaeton without being told why. And now Phaeton sends us his Neo mega pets." The shuttle has landed and opened, walking down the steps is one Neo mega in the lead with four behind that wear white and surround a container. As the Neo wearing purple walks to Draconis, Draconis greets him, "Lysander, welcome to Venus. I and my staff are at your disposal, as Phaeton directed." He responds tersely, "We have no time for protocol Draconis; is our transport ready?" Annoyed, Draconis replies, "Of course." As they walk to the transport Lysander asks, "Have the requested specimens been isolated?" Draconis tells him, "I've prepared a special facility for them, as Phaeton ordered, on Mount Artemis." They have arrived at the transport and after the four Neos with the special container enter it Draconis says, "I'd, uh, like to know the purpose of your mission." As Lysander enters the transport he tells him, "Your duty is to provide security, you do not need to know anything more." Draconis can no longer conceal his anger, and he shouts, "I command Venus, I will know what you're doing!" Lysander turns back and says, "Unlikely." Draconis then turns to his aide and tells him, "Creon, find out what Lysander's up to, then report back to me." Creon salutes and boards the shuttle. Draconis has a smile that appears both devious and confident.
In Venusian orbit, a Pirate ship is shown decloaking. Some e-frames exit and the ship quickly recloaks. The e-frames of Able Squad enter the atmosphere, and begin to move down among the clouds. Marsh announces, "Stay alert, people." Nara Burns is watching her sensor screen and sees, "Multiple targets, three Neo e-frames at nine o'clock." Marsh responds, "I see 'em." A Neo y-wing is in the lead, and it opens fire. Trailing it on either side are a purple high speed stealth e- frame and a blue command e-frame. Marsh quickly orders, "Spread formation!" and Able Squad scatters as the shots fly by. The y-wing chases Marsh, but he turns and fires one of his turbine missiles to destroy it. The other two Neo e-frames fire repeatedly as they chase Wolf Bronski. Wolf yells, "He's on me, can't shake 'em!" Rita Torres tells him, "Break right, Bronski!" and it gives her the angle she needs to destroy the blue Neo e-frame. The remaining Neo stops, and then begins to fly off. Kaz Takagi shouts, "He's running for it!" and begins to give chase. But Marsh says, "Let him go Takagi, break off pursuit. We're here to look, not fight." Kaz breaks off and returns to the squad, saying, "Hey, can I follow orders or what?" A smiling Torres tells him, "Takagi, only you can show off by not showin' off." Marsh tells the squad, "Let's get down to the surface before any more Neos show up." And the squad proceeds down through the final layer of clouds.
At a Resistance installation overlooking the Sea of Amon, Able Squad sits with some members of the resistance around a fire. Marsh tells them, "We're here to do a complete recon of Venus. We've got to locate every Neo base and troop concentration and report back to ExoFleet." James Burns has a bit of excitement in his voice, "That can only mean one thing, ExoFleet's gettin' ready to liberate Venus." Between sips of his coffee Marsh says, "I, uh, can't confirm anything." James stands and tells him, "We just want the chance to take back what belongs to us... our homes, our planet." The other resistance members nod and voice their affirmation. Marsh tells him, "You'll get your chance James, and maybe sooner than you think." James says, "We've almost been wiped out, there's just a handful of resistance fighters left, but we'll give you everything we've got." Nara, sitting next to her brother, reaches for his hand and tries to get his attention by saying, "James." He looks at her and says, "I know we'll win Nara. We'll make the Neos pay for everything they've done. We'll make them pay for Mom and Dad." She looks up at her brother sadly, and then drops her head.
Nara and Marsala's e-frame breaks the surface of Lake Uris near a Neo fortress. Marsala says, "Heavy fortifications." They resubmerge and Marsala asks, "Can you estimate troop numbers from the sensor scan?" When she doesn't answer he asks, "Nara, is something wrong?" She replies, "I'm sorry, I was just thinking. James has been through so much, sometimes I feel like I don't really know him anymore." Marsala tells her, "No matter how James has changed, inside he is still your brother." "Thanks, Marsala." He then says, "Now, about those troop numbers." As she activates a sensor console Nara says, "Oh, right."
At Dragon's Rock, James Burns flies with Alec DeLeon and Maggie Weston. James tells them, "Half the people who escaped from here are gone now. When I get my hands on Draconis..." Alec interrupts, "We've got no time for revenge, James, fighting the war comes first." Weston reiterates, "DeLeon's right, this isn't a personal vendetta." James tells them, "You wouldn't say that if you'd lived through the occupation. This is personal, between Draconis and me."
Bronski, Torres, and a guide from the resistance are walking up a slope on or near Mount Artemis. Bronski complains about the surveillance equipment they carry, "Man, why do we have to lug this junk up the mountain on foot, that's what e-frames are for. If I'd a wanted to walk I'd 've joined the infantry." Torres tells him, "Can the complaints, Bronski, and keep climbing." A short while later their guide, who looks like the resistance member we come to know as Krueger, gasps as he points, "We're here. Fort Elizabeth." Bronski looks and says, "It's kinda pretty, you wouldn't even know there were any Neos in it." With hatred in his voice the guide says, "I'd know." Torres has already started to get to work, and she tells Wolf, "Come on Bronski, let's get this equipment set up." He replies, "Yeah sure thing, Sarge."
They set up the telescope and Bronski plays with it a little, asking, "How do you work this thing anyway?" As he looks through it at the Neo camp he soon sees what looks like a flying security camera and he shouts, "Neos!" Torres dives for a blaster and shoots it out of the sky. Torres shouts, "Forget the equipment, clear out!" and as they leave they begin to come under fire. Two Neo y-wings emerge nearby and open fire. Soon their shots cause a small landslide, and with the rock beneath his feet gone Bronski falls as Torres watches and shouts his name. Bronski lands hard and begins to get up, saying, "Oh man, if there's anything I hate worse than walkin', its fallin'." A searchlight then blinds him , and he covers his eyes. As he gets up Creon's voice is heard, "Don't move Terran, you are surrounded." Bronski looks around and then dives behind a nearby rock. He is able to duck around the rock and shoot out a couple of the searchlights.
Meanwhile Torres and the resistance member are hiding behind another rock and coming under heavy fire. Torres contacts Marsh, saying, "J.T.! We're taking fire, at least two Neo e-frames. Bronski's been down at the base of the cliff." Marsh responds, "Hang on, Rita. We're on our way." He, Takagi, and a number of others in e-frames then leave their position to go and assist.
Torres and the resistance member shoot back at the waves of Neo y-wings, but it does little good and one of their blasts knocks Torres on her back. As a Neo moves in for the kill it gets destroyed by Takagi. Torres looks up and sees him, and Kaz gives a thumbs up as he says, "Score one for the cavalry." Below, Bronski dodges multiple shots from various locations, saying, "I knew we shoulda brought our frames." Soon he finds himself right in front of a Neo hovertank ready to fire, but he dodges before it shoots and a missile from Marsh soon hits it. Marsh tells him, "Climb on Bronski." He holds out his e-frame arm, but gets hit there and is knocked back into the cliff face. He slides down to the bottom and is soon the target of a Neo hovertank. As the hovertank approaches the turbines on his e-frame try to restart but fail, and he says, "I can't get reignition."
In the sky above a battle rages. Another squadron of Neos approaches and Kaz says, "We've got to get out of here, J.T.! There's too many of 'em!" Marsh watches two hovertanks close in on him and responds, "Pull everybody out of here, Takagi." As the two hovertanks begin to round a corner, the green two-seat e-frame decloaks behind them and fires a few shots and missiles to destroy them. Nara says, "We'll hold 'em off, J.T." Marsh is back in the air and tells them, "Nara, Marsala, am I glad to see you. Keep their heads down while we withdraw." Marsala replies, "Understood, J.T." Marsh flies over to pick up Bronski and then takes off with him. Torres and the resistance member are likewise picked up by others, and they all begin to flee.
Nara says, "They're clear Marsala, let's go." At that their e-frame lifts off, but is soon hit by shots from a pair of hovertanks. Nara shouts Marsala's name and he responds, "We're going down." They crash and the two quickly exit and run for cover. A hovertank shoots a bend in the canyon where the two had just run, and propelled fragments of rock knock Nara and Marsala to the ground. James sees this, shouts his sister's name, and lands nearby. Nara groans as James tells her, "Climb on, Nara." The left arm of his e-frame is hit by a shot, surprising him. He picks up his sister's body and flies off. Marsala, who lay not far away, watches and says, "Go safely, Nara Burns." Creon shouts at Marsala, "Surrender!" Marsala turns to see a number of Neo guards with blasters pointed at him. Creon approaches and says, "The famous Marsala, at last." Marsala looks at him with a bit of anger on his face.
Marsala is then inside the secret Neo sapien facility, which has corridors and doors like the ones in his dream. Creon walks ahead of him, two guards are behind. At one of the doors Creon holds up his hand and orders, "Halt!" He looks inside the cell and is shocked by what he sees. Marsala looks inside and sees a blue figure whose skin is apparently gelatinous, as his head is conical and the skin itself seems to be slowly flowing downward. The figure moans, and Marsala is taken aback, observing, "AutoMutation Syndrome!"
Lysander approaches them, saying, "Yes, the fear that haunts every Neo sapien. The manipulated genes of Neo sapiens are inherently unstable. Cell damage can trigger AutoMutation, but injury is not necessary for AutoMutation to occur. It can strike any Neo sapien at any time, even traitors." Marsala's look changes to that of horror. Creon tells the guards, "Lock him up!" and they take Marsala to an empty cell and throw him in. Marsala is left alone with the wailing and cries of agony that come from the from the other cells.
Creon is reporting to Draconis, whose image is on a viewscreen. Creon says, "The traitor Marsala has been captured, I am holding him for questioning. I've also found out what the Neo megas are..." As he is saying these words Draconis'face disappears and is replaced with that of Lysander, who says, "I warn you Creon, there will be no unauthorized communication. Is that understood?" The viewscreen then goes blank, and a angry Creon is left sitting there.
A shuttle is shown arriving at the research facility. Inside, Lysander and two other Neo megas observe a chemistry lab setup, when Draconis and two guards enter from a door at the far end of the room. Lysander turns to look and says, "Phaeton has ordered the base closed, you have no authorization to be here." Draconis responds, "I command Venus, you have an ExoFleet prisoner, that's a military matter. And this base is under military protection, I demand to know what I'm protecting." With a contemptuous look Lysander replies, "You don't have the authorization, or the intelligence." Draconis raises his arm, and his guards take aim with their blasters. Draconis says nonchalantly, "I'd hate to have to tell Phaeton about your unfortunate laboratory accident." Lysander tells him, then his own assistants, "Very well, you'll have your demonstration. Prepare the next specimen."
Back at the Venusian resistance base Kaz tells James, "You shoulda pulled Marsala out when you picked up Nara." James, sitting with his sister, replies, "There was no time. And I couldn't risk my sister's life to try and save Marsala." Kaz shoots back, "You just didn't want to try because Marsala's a Neo sapien!" With a response of, "Oh yeah?" James shoots to his feet and begins to struggle with Kaz. Marsh pushes the two of them apart, saying, "Hey, break it up you two."
Bronski's head is bandaged and he says, "Ah it's all my fault, if I hadn't tripped over my own big feet." Torres offers him a canteen and tells him, "You did the best you could Bronski, we all did." Bronski takes it and drinks some of the water.
DeLeon walks over to Marsh and says, "Draconis will question Marsala, if the Neos learn about our plans to invade Venus the whole operation could be a failure." Marsh asks, "You think I haven't thought of that?" DeLeon continues, "There's only one way to make sure Marsala isn't forced to talk." Marsh finishes the thought, "I know, we may have to destroy the base, with Marsala in it."
This upsets Nara, "I don't believe this, we can't sacrifice Marsala just because he was captured?" Marsh tells her, "Nara, we can't risk Marsala telling Draconis about the invasion, and the Neos can make anybody talk." With an angry look Nara states, "Not Marsala." Marsh asks her, "Do you want to take the chance with the lives of everyone in the ExoFleet?" Nara says, "We've got to rescue him!" Marsh explains, "Half our e-frames are damaged or destroyed, there's no way we can fight our way into that base. It's too well protected." No less unhappy Nara asks, "So that's your decision?" Marsh tells her, "It has to be."
At that Nara walks over to her personal e-frame. As she climbs in her brother asks, "Where are you going?" She replies, "As far away from here as possible." She then flies off.
Marsh watches her leave and says, "Maggie, you and DeLeon collect the fusion packs from the remaining e-frames. Rig 'em to detonate on impact." As the begin to go DeLeon tells her, "Put them on my frame." Marsh holds his hand up to signal them to stop and he says, "No, this was my decision. I've got to do it."
Back inside the Neo research facility, two Neo mega assistants strap a Neo with AutoMutation Syndrome to a table as Creon, Draconis, and Lysander watch. There is no cohesion to the subject's skin, and his face is not visible. Lysander says, "I've combined the mutating agent with a compound to stimulate brain activity." He goes over to the container that was taken from the shuttle to the transport. As he opens it he continues, "To restore the body's structure to its normal state." He removes a smaller container which holds several vials of a blue liquid. He places one of the vials in an injection gun, walks over to the test subject and gives him an injection. He says, "Sterilize it immediately. A single molecule would be enough to trigger mutation in a healthy Neo sapien." The Neo on the table returns to a healthy form, but only for a moment. Soon he is shown sprouting three arms from his chest, as Draconis and Creon look on in horror. Crying out in great pain all the while, the subject's body soon oozes back to its AutoMutation form. Lysander just shakes his head and says, "Another failure. Take him back to his room."
Draconis then says to Creon, "If a single drop is as powerful as Lysander says, then the mutating agent could be a devastating weapon. Against Terrans... or Phaeton and his supporters, when the time comes." Draconis then steps forward as the previous subject is taken away, "One more test, Lysander. A healthy Neo sapien this time, the renegade Marsala. Maybe death will loosen his tongue about ExoFleet plans."
Nara sits on a rock formation, overlooking a fairly barren area. The sun has just set, and Nara says, "Marsala, I can't let this happen to you. You saved my life, I've got to try and save yours. Even if it costs me my own." At that she stands and takes off.
Back at the resistance base, Maggie finishes hanging the fusion packs on the missiles of Marsh's e-frame. She tells him, "Fusion packs are all rigged, J.T." Marsh, who is already inside, says, "Stand clear." He powers up his e-frame and takes off, exiting the base.
Marsala sits in his cell. The door opens and he gives an angry look to those standing outside. Draconis points to him and then motions back, saying, "You, out." Marsala stands and walks out. As he does so Lysander and two other Neo megas walk by, wheeling along the last subject. Draconis says to Marsala, "Unless you tell us everything you know about ExoFleet plans, you will be the subject of their next experiment." Marsala responds, "I cannot betray my friends." Draconis tells him, "Then you share the same future as this thing. Take this traitor to the AutoMutation lab." Marsala walks away with the guards.
The Neo megas have left their last subject in his cell, and so they do not see when he lets out a groan and changes shape to take the form of Lysander.
Just outside the facility Nara lands and exits her e-frame. When she hears something flying overhead, she leaps out of view. Meanwhile, J.T. Marsh is flying to the research facility.
Marsala is now strapped to the table. Draconis leans over to him and says, "Marsala, once again, what are the ExoFleet plans?" Marsala just turns his head away. Draconis orders, "Prepare the mutating agent."
Outside, Nara makes her way to the facility. A guard approaches her from behind and shouts, "Halt, Terran!" She quickly turns and fires, hitting him. She then runs toward the facility, and a guard sees her and takes aim. Just then, Marsh launches his first missile, causing a large explosion that causes many pieces of rock to begin falling. The Neo who had been aiming for Nara is forced to move to avoid being crushed. Nara continues, dodging falling rocks as she finds and entrance and makes her way inside.
The ceilings on the interior of the facility are a source for falling rocks inside. The inmates now yell in panic. Two Neo y-wings launch before falling rocks close up the entrance to the hangar. They approach Marsh, who looks at them and says, "This is for Marsala." With a glow of his cyberjack he initiates a solar flare that destroys the two y-wings as well as an upper corner of the building. He launches a few more missiles at the facility, and inside rocks continue to fall and it seems obvious that the entire structure is about to collapse. Guards begin to scatter. Elsewhere, Nara is shown going through a doorway. In the testing room, the Neo megas run off, leaving Marsala strapped to the table, struggling to get free.
Nara is now nearby, and she calls out, "Marsala, where are you?"
A Neo from one of the cells, likely the one that had just been experimented on, pushes out the cell door and exits. Draconis, Creon, and the Neo megas flee down a corridor. When a large collection of rocks fall on the Neo megas, Creon turns to help a struggling Lysander. But Draconis tells him, "Let the Neo megas look after themselves." The two then leave. The Neo with AutoMutation syndrome then approaches Lysander who looks at him with shock, saying, "You! No!" The Neo falls on Lysander, and the two meld together. A single large gelatinous form stands, and with some groaning and growling takes the form of Lysander.
Draconis and Creon run to a shuttle, enter, and fly out of the facility.
Marsala is still struggling to escape his restraints, when Nara comes running in. She shouts, "Marsala! The whole mountain's coming down!" She helps him get free, when the Neo in the form of Lysander attacks from behind. Marsala sees him and shoves Nara out of the way, yelling, "Look out!" Marsala struggles with him, and Nara shoots him causing him to become unconscious. Marsala lifts him over his shoulder and tells her, "We'll take him with us, and that container." Nara grabs the container with the vials and the two of them run out.
Outside Marsh is finishing off the building. One final shot and it all collapses to the ground in a large explosion. Nara and Marsala have gotten out safely, and Marsh flies to where they are running and lands his e-frame in front of them. He says, "Ha! Marsala, I thought I'd never see you again. Oh, glad I was wrong. And you, Lieutenant Burns, good job." Nara doesn't seem to know how to react to that. Marsala swings the Neo in the form of Lysander off of his shoulder, looks at him and says with some sadness, "We have looked into the face of our greatest fears, and found... ourselves." Marsh just says, "Come on, let's get back with the squad. Where we belong." They all leave, behind them are the remains of the research facility.