In "Crossfire", the second season finale, Liam Kincaid, Jonathan Doors and Augur had taken refuge in an apartment and were about to be captured by a team of Volunteers who were rounding up Resistance members after martial law had been declared on earth. On the mother ship, Captain Lili Marquette had obtained access codes for the ship's power system, and was poised to destroy the ship and everyone on it. Lili contacted Liam Kincaid at the apartment where he, Augur and Doors had taken refuge, and told him that she had gained access to the ship's power system and was about to overload it. Liam was horrified and told Lili that what she was about to do will kill everyone. Lili told him that the prisoners would be forced to talk anyway, and the Resistance would truly be dead. Doors was in agreement with Lili about destroying the mother ship. At that moment the sounds of blasting were heard outside the apartment and contact between Lili and Liam was broken off.

In the opening scene, the Volunteers burst into the apartment where Liam, Doors and Augur are hiding and tell everyone to get down. The team leader tells one of his members to get Doors out of the apartment, and he is hustled out, leaving Liam and Augur behind.

One of the other volunteers asks where Doors is and is told that Doors is on his way to the mother ship. There is some confusion because the volunteers recognize Liam as Da'an's protector, but he is placed under arrest anyway, and he and Augur are led from the apartment by one of the volunteers who is female.

Liam, Augur and the volunteer leave the apartment amid weapon fire and confusion. The volunteer is acting in an evasive manner and Liam asks her what she is doing. The volunteer replies that questions will have to wait, unless they want a one-way ticket on a Taelon transport, adding that Zo'or would be glad to see them and addressing Liam as "Major". She tells them to remember to act as though they are her prisoners, to keep their heads down and make it look like they are under arrest. They go around a corner of the building. Liam and Augur look back at the front of the building, and when they turn again, the volunteer is gone.

Augur comments that the volunteer is his kind of woman, saves his ass and doesn't even leave a phone number so he can buy her dinner. Liam says that they will have to track her down to thank her in person and suggests they leave the area.

On the mother ship Lili has already overloaded the ship's engines, and is trying to reestablish contact with Liam when she is discovered by a security team and hustled out of the mother ship's main control room.

Sandoval informs Zo'or that Lili has overloaded the ship's engines, and Zo'or tells him to override the command. Sandoval and the technicians are unable to do so because Lili has locked them out of the system. Zo'or tells them to shut it down manually and is told that the fusion reactors are crystallizing. An engine has been lost, and the commander of the security team orders immediate evacuation. Sandoval orders everyone to remain at their stations, but decides to evacuate immediately when he is told that the ship is going to blow. Zo'or is standing motionless, and Sandoval makes the mistake of seizing Zo'or's arm and attempting to hustle him off the ship. Zo'or's reaction is volcanic. He tells Sandoval to take his hands of him and throws him to the floor. The startled Sandoval protests that it is his job to protect Zo'or, and asks what Zo'or, who has moved to the mother ship's main console, is doing. Zo'or replies that he is excising the problem. He presses a button on the main console and the overloaded components are ejected from the mother ship in a shower of sparks.

A news broadcast is in progress and the announcer relates that hundreds of suspected Resistance members have been apprehended after the attempt on President Thompson's life. There is still no word from the White House on how long the state of emergency will last.

Liam and Augur have returned to the former Resistance headquarters which is now Augur's home. Liam says that it appears that the underground's entire network has completely collapsed. Volunteers are pulling in people who have never even questioned the Taelons. If the state of emergency isn't lifted soon, he and Augur may be the only people left in the Resistance. He asks when Thompson's news conference is scheduled to take place. Augur replies that the news conference is scheduled to take place in three days and that Thompson is going to release the name of the man who tried to assassinate him. Liam believes that their only hope is proving that whoever shot Thompson is not on their side. Augur is still not sure that the assassin wasn't a Resistance member.

Liam asks if there has been any word from Lili. Augur says that Lili can handle herself, and Liam replies that it is not Lili he is worried about, it's the rest of the world.

On the mother ship a young female volunteer tells Sandoval that she has taken care of the little problem as he requested. Sandoval says that he trusts she will keep him informed up to the very last minute. The volunteer demurs and says that she wouldn't want him to miss a thing.

Sandoval tells Zo'or that the mother ship will need to operate on auxiliary power until they can repair the damage, and tells Zo'or that a team of volunteers are already on their way. Zo'or tells him to send them back to their duties as they are of no use. The mother ship is and organically-engineered life form and was designed to regenerate itself. He then moves on to the subject of Lili Marquette. Sandoval asks if Zo'or has something special in mind, and Zo'or nods. Sandoval contacts security and tells them to bring Lili to the bridge, but is told that it is not possible.

In Augur's apartment, Liam and Augur are searching the computer for information on the woman who rescued them and are unable to discover anything. Liam says there has to be something on her somewhere, and Augur says that she is either ex-volunteer, lone operative, or belongs to some radical cell they haven't heard of. Liam says that she saw their faces and knows their names. For all they know, she could be a Taelon double agent. Augur is attempting to model the face of the unknown female on his computer screen and tells Liam to have patience.

A news bulletin interrupts Liam and Augur's conversation, saying that there has been an explosion on the mother ship which was sabotaged by Captain Lili Marquette. She is identified as a decorated marine and a top Taelon shuttle pilot. Captain Marquette was killed in the blast, along with thirteen others including the East European Companion. Additional news will be broadcast as it comes in. Augur breaks down entirely, saying that the bastards killed Lili. Liam tries to console him, but Augur has no desire to be comforted. Liam's face is a study in grief and anger as he says in disbelief that Lili is gone.

At the embassy, Liam tells Da'an, who is looking out the window, to turn around because he wants to see Da'an's face. Da'an asks what will happen if he does not - will Liam try to kill him as Captain Marquette did? Liam replies that if he wanted to kill Da'an he would already be dead. He says that Lili never wanted to harm Da'an. Da'an replies that an attack on any Taelon is an attack on the Commonality. Liam tells Da'an to blame Zo'or, that this would not have happened if Thompson had not declared a state of emergency. Da'an replies that it was the President who instituted these measures. Liam shrugs off the comment, saying that Thompson can't even take a walk without Zo'or's permission.

Da'an asks what would have happened if Jonathan Doors had been the target of an assassination attempt and what measures the Resistance have called for. He accuses Liam of blaming the Taelons for the tragedy when humanity cannot even control its own members. Liam says that the Resistance didn't shoot Thompson. When Da'an asks how he intends to prove it, Liam tells Da'an to "just watch me". Da'an is very distressed and attempts to regain control of the meeting, saying that he has not assigned Liam to that investigation. Liam replies contemptuously that he is not asking for Da'an's permission and leaves the room.

A group of volunteers are standing near a port on the mother ship when Liam bursts into the chamber. He identifies himself, asks what they are doing and inquires who is in charge. He is told that the volunteers have instructions to dispose of Lili's body which is lying on a gurney by the port. There is a brief confrontation in which Liam refuses to allow the volunteers to dispose of the body into space through the port.

Sandoval enters the chamber and asks Liam what the problem is. Liam says that he is taking Lili Marquette back to earth for a proper burial and a full autopsy. Sandoval says it will not be possible because rules are a little different in space. He doesn't necessarily agree with them, but Captain Marquette committed an act of treason, and the Taelons have the right to bury her body as they wish. Liam makes the observation that it isn't the Taelons, but Zo'or specifically who are doing this. Sandoval tells Liam that he understands and even shares his grief. When Liam begs Sandoval not to dispose of Lili's body as planned, to let him take it and that no one has to know, Sandoval says that he wishes matters could be different, but there's nothing he can do under these difficult circumstances. Liam wishes to make a final identification and tells Sandoval that it is his way of saying goodbye. Sandoval cautions Liam that some things are best left unsaid and unseen. When Liam says that this is one memory he would like to keep, Sandoval remarks that the problem with memories is "that once you have them in your mind, it's very difficult to ever get rid of them". The grief stricken Liam unzips the body bag and looks down at the bruised face of Lili Marquette. He is overcome by emotion and unable to speak.

Sandoval encounters Hubble, President Thompson's chief of staff at the auditorium where the attempted assassination took place. Hubble says that he was told that they would have conclusive evidence this afternoon so the president can make an announcement the following day, and that now he is getting a Taelon tap dance. Sandoval says that the FBI is ready and that they are waiting for the medical examiner, a man named Anders, to corroborate the evidence. Hubble suggests that they hurry Anders along.

On the mezzanine level of the auditorium where the assassin was situated, and where he was killed by a blast from Sandoval's skrill, Anders is taking samples, and says aloud that with all this new Taelon technology, the least they could do is improve these damn lids. Sandoval offers to provide him with whatever he needs, and Anders, who is obviously acquainted with Sandoval, says that he is kind of old-fashioned and likes to do the dirty work himself, especially with a case as high-profile as this. He wouldn't want to screw up anything with the Feds looking over his shoulder and all. He asks Sandoval to confirm that the assassin shot the president from the catwalk, and asks if that is where the remains were found. Sandoval is impatient and says they have already been over this. Anders says he just wants to make sure that he got it right with so many people dying, and so little time. He is curious to know why Sandoval is interested in what he thinks since a preliminary DNA test has already been run on the shooter. Sandoval says that given the sensitive nature of this investigation, they want to make sure that all bases are covered. After all, it isn't every day that the President gets shot. He want to know Anders's findings before any statements are made. Anders says that the last time he checked, he reported to the mayor, and not to Sandoval.

Liam enters the auditorium and speaks to Anders, asking him how the collection business is. Anders tells Liam that the Feds don't leave much behind. There is a brief discussion about the fact that ballistics tests can not be run on skrills and that forensics seems to be a whole new ball game these days. Liam asks how Anders manages to keep genetic samples from degrading and is shown an ordinary picnic cooler. When Anders leaves for a moment to confer with a colleague, Liam helps himself to one of the samples from the cooler. An agent named Tate approaches Anders and says that Sandoval wanted to make sure that he has everything he needs. Anders comments sarcastically that he didn't know the FBI could be so kind.

Augur and Liam are together at Augur's flat, and Augur asks how Liam is holding up. Liam replies that he keeps seeing Lili lying on the gurney, and that one always thinks people look like themselves when they die, but they never do. One tries to remember the good and all that went before, but it's always that last image that grabs one the hardest. Augur says that it will pass, and Liam says that he is not sure that he wants it to, because then Lili is gone forever. He asks if Augur can pull a DNA code from the sample he has provided, and Augur says that one double helix scan is on the way. The sample is identified as belonging to Albert Phillips, who is a Resistance member. Augur says that Sandoval was right; the Resistance did shoot Thompson. Liam is shocked and tells him to run the DNA sample again. When Augur says that DNA doesn't lie, Liam says that he doesn't care - run the sample again and find him someone he can talk to who knew Phillips.

On the mother ship a volunteer escorts Zo'or into the chamber where Doors is being held. Zo'or tells the volunteer to drop the confinement shield and leave them alone. Doors wants to know what has been done with the other prisoners. Zo'or asks if Doors is getting lonely for human companionship and tells him that the world as he knows it has changed since his incarceration. When Doors asks what that means, Zo'or tells him that the Resistance exists no longer and that the same can be said of some of his dear friends. He suggests that they discuss a mutually beneficial alliance.

Sandoval meets Agent Tate secretly, and they discuss the uncooperative Anders. Sandoval says that this unexpected complication in their plans will have to be alleviated. Agent Tate casually asks when he wants to take care of their forensic friend and says that since it is after hours there will be overtime. Sandoval tells him to call his union.

Liam Kincaid is standing in a park near a hot dog stand. He identifies himself and asks its attendant if she is Emily Langford. An announcement has just been broadcast that curfew time is approaching and all citizens must be in their homes. Liam tells Emily he is looking for Albert Phillips, and she tells him that his Taelon bosses took Albert away over a month ago. Liam tells her that tomorrow the president will announce the name of the assassin, and the assassin has been identified as Albert. Emily laughs bitterly and tells Liam that Albert was a pacifist, before saying that nobody cares about the truth any more and leaving the park.

Anders calls Liam and congratulates Liam on the way he lifted the DNA sample, with no less than a dozen FBI agents around. He comments that Liam must trust Sandoval as much as he himself does. Liam is non-committal. Anders says that his interpretation had better be right because he is betting on Liam. Liam is still noncommittal and pretends not to understand. Anders says that Liam will understand later and asks him to come to his office " if he has an interest in the real facts of the case". They arrange to meet in fifteen minutes, and Anders asks Liam not to be late because he can't keep the findings from the FBI forever. Liam cautions Anders and says that Sandoval may already know. Anders says that he will back up his records in case anything happens to him. He hangs up and makes a copy of the material he is working on, tucking it in the bottom of a box of cigars. He then leaves his lab and walks down the , and we see Agent Tate loitering in the corridor, dressed in a lab coat. When Anders walks into a morgue a few minutes later and slides open a drawer containing a body, a hand (that of Agent Tate) reaches up and strangles him.

Liam arrives at the forensic labs and identified himself before being admitted. He hears Anders screaming and runs to the storage room where he sees agent Tate running away and finds Anders dead.

President Thompson is surrounded by volunteers when Hubble approaches him. A volunteer tries to stop Hubble who identifies himself and tells the volunteer to stand aside before he (Hubble) rips the damned implant right out of his neck. The volunteer apologizes and gets out of the way.

Thompson and Hubble get into the limousine togther and drive off. Hubble says that he is beginning to have concerns about the state of emergency, but the president is only interested in his ratings (which haven't been this high since he bombed the Irasian Republic). Hubble says that there are volunteers everywhere, that he doesn't like it and that neither will the rest of America when they realize they're living in a police state. Thompson says that the state of emergency is a temporary measure to destroy the Resistance. Hubble cautions Thompson not to cut off his own legs too. Thompson says that he knows what he is doing and that he is doing what the voters want. Hubble replies sarcastically that Thompson is simply doing what Zo'or wants and reminds Thompson that he is talking to his advisor, not to a camera. He tells Thompson that one day he will have to stand up to Zo'or before it is too late to draw a line in the sand.

Augur is still trying to find out who their mystery rescuer is and is modelling her facial image in his computer. He tells Liam that when he has finished, he will run the image on every database he has. Liam says that Augur has seen what she can do and tells him that he had better be two steps ahead of her, but Augur thinks that the mystery woman can't hide forever. Liam asks him to run another DNA test, a simple dating analysis on Phillips. They do so and Augur is surprised to learn that Phillips was supposedly killed a few days ago, but that the sample taken from the auditorium is over a month old. They decide that the sample was planted and Phillips was framed. Liam thinks that the real assassin's remains are still in the auditorium. Augur is dubious because Sandoval's men will have cleaned up everything by now, but there is one remote possibility which is worth examining. Sandoval killed the assassin on the catwalk, and it is possible that the energy from the skrill created a molecular bonding which fused the assassin's DNA to the metal of the catwalk. If so, Liam will be able to obtain another sample which indicates who actually fired at Thompson. To cover their tracks completely, Sandoval's team would have to remove part of the catwalk altogether.

Liam goes back to the auditorium and starts to mount to the catwalk. Agent Tate is there before him and has placed an explosive device on the catwalk, activating its timer. He noticed Liam approaching and leaves the auditorium. Just before the device goes off, Liam notices it and slipping between the boards of the catwalk, he hands suspended on a rope below the catwalk as the blast occurs. When the explosion has ended, he pulls himself painfully (but unharmed) back up to the catwalk. The segment of the catwalk where the assassin was killed by Sandoval has been scoured by the blast.

Liam returns to Augur's apartment and gives him the samples he was able to obtain from the auditorium. Augur remarks that bombs are an effective way to clean up a crime scene, and that Liam's sample is not in good shape. They are both hopeful that the sample confirms that Phillips really wasn't the killer. Augur runs the sample through his computer, and to their surprise, they learn that the assassin was Judson Corr, the hired gun who killed William Boone's wife, and who is occasionally hired by Sandoval for freelance assignments.

Liam approaches Hubble, Thompson's chief of staff, about the upcoming announcement from the president on the assassin's identity. Hubble compliments Liam on the fine job done on the investigation. Liam hands him a disk containing the DNA evidence and tells him that the FBI findings which Hubble has already received have been faked. He fills Hubble in on the true facts, including Albert Phillips' abduction by the Taelons a month previously, and the identity of the real assassin, Judson Corr. Hubble is not convinced and Liam tells him that there is also a dead coroner and a destroyed crime scene to be considered as part of the scenario. He also utters a veiled threat about the information being leaked to the press and says he is looking forward to the president's speech.

Augur has finished his computer portrait of the mysterious woman and is happily running it through his databases. In an office in another part of the city, the woman looks at her computer console and remarks aloud that Augur is ahead of schedule and that it is good work, but not good enough. She smiles and presses a key on her keyboard. Augur's computer systems all crash simultaneously. Augur realizes what has happened and remarks aloud that he has to meet this woman.

Hubble contacts Liam to say that his people have examined the evidence which is impressive, but he can't take it to the president because the genetic samples on which it is based could have come from anywhere. Liam says that he collected the evidence from the auditorium himself. Hubble remarks that the catwalk is toast and that there is nothing to validate Liam's findings. Liam asks Hubble how he explains the presence of the DNA sample. Hubble says that he could find forensic experts who would testify to the fact that the DNA was tainted. He leaves after asking Liam to call him if anything else was found.

Thompson and Hubble are discussing recent events. Thompson is exuberant because his audience loved the speech and his new lead-in. Hubble is noticeably glum, and Thompson asks him if there is anything he should know. Hubble says, "No, not yet".

Augur has checked Anders's computer and others on the on the same network and found no trace of Anders' work. Liam is worried because the president goes on air in less than four hours and they still haven't found anything else. Augur thinks that perhaps Anders never backed up his findings onto disk, but Anders' assistants had told Liam that he was a stickler for keeping records. Augur thinks Anders may have forgotten to back up his work, but Liam thinks otherwise. Augur points out that DNA can't be stored just anywhere, that it needs a stable temperature, and they have already checked all the refrigeration units.

Hubble meets with President Thompson who has been speaking with the speaker and senate majority leader. Thompson is ecstatic about his speech for the upcoming press conference and Hubble tells him he will have to throw it out. Hubble tells Thompson that he should see Major Kincaid.

Thompson's long awaited press conference begins and he tells the American people that he had fully expected at this time to confirm the identity of the assassin who shot him, but new evidence has been found which casts serious doubt on the theory that the assassin was part of the Resistance. In accordance with the War Powers Act of 2004, he has no choice but to rescind the state of emergency. He orders the immediate return to earth of all suspected Resistance prisoners being held on the mother ship.

On the mother ship Zo'or and Sandoval are watching the telecast, and Zo'or is outraged. He tells Sandoval to bring the incompetent fool to the mother ship at once.

Da'an and Liam are also watching the newscast and discussing it. Da'an asks Liam who really did shoot Thompson since it appears that the Resistance did not. Liam speculates that Sandoval arranged the scenario with Zo'or's permission. Liam turns to leave and Da'an asks him where he is going. Liam says that he wants to make sure that every prisoner gets back to earth. Da'an says that it is not necessary, and Liam replies that with Sandoval around, people have a way of disappearing.

On the mother ship Zo'or is meeting with Thompson, and tells him that rescinding the state of emergency showed disrespect for the Taelons. Thompson is angry and snaps back that Zo'or had the audacity to risk his life, and perpetrate a fraud on the American people, and that he has no right to accuse him of disrespect. Zo'or serenely replies that if he had not commandeered the election, Jonathan Doors would now be president, but Thompson refuses to believe that. Sandoval says that perhaps Thompson should consult his polling organization. Zo'or says that the state of emergency is now irrelevant, and that what is most important is that the volunteers remain on earth until the Resistance is eliminated. Thompson refuses to sanction the volunteers remaining on earth, and Zo'or says that his permission is not necessary. Thompson says that the time has come to redefine the parameters of their relationship. Zo'or replies that the only reason Thompson is in the White House is because the Taelons put a bullet through his shoulder, and that next time, they may not aim so carefully. Hubble is standing in the background, wearing an "I told you so expression".

A volunteer says that all Resistance prisoners have been accounted for and returned.

Doors has been released and meets with Liam, who tells him that the Taelons killed Lili. Doors expresses his condolences. Liam says that it is time to put their differences aside, and Doors says that he has to work in his own way.

On the mother ship, Doors meets with Zo'or who says that he looks forward to their association and has no doubt that it will benefit both their species. Elsewhere on the mother ship, Liam meets with Sandoval who tells him that he has an assignment for him, a personnel problem. The night Doors was apprehended, a woman disguised as a volunteer killed a member of her unit and allowed two unknown suspects to escape (actually Liam and Augur). Liam makes a remark about the incident being a serious breach of security. Sandoval says that every companion protector around the world is investigating. He is worried about the knowledge that the unknown woman may have gained of their operations.

Barry Calvert, a newscaster, reports live with the first broadcast ever from the Taelon mother ship. Z o'or is introduced as the leader of the Taelon synod and arguably the most powerful being in our galaxy. Zo'or has an announcement to make to the American people and introduces Jonathan Doors as his esteemed associate. Doors thanks Zo'or and tells the viewers that for those who supported his presidential campaign, the sight of him standing next to his former enemy must be shocking. He says that the time has come to put petty differences aside, and that although differences remain, the Taelon presence on earth has overwhelming support. Calvert asks if he will be distancing himself from the ideology of the Resistance. Doors replies that the issue was never really the Resistance. The issue is, and always will be, what's best for humanity, and that is why Doors International has formed a new alliance with the Taelons. Liam who is watching, makes a disgusted comment about one big happy family. Doors says that it is time his company got back to what they had started four years ago, using the best of Taelon technology in everyday earthly applications. Calvert says that it seems Doors will have a lot on his plate this coming year, and Doors says that the work will be in the capable hands of his new division head, Renee Palmer. He introduces her to the press conference. Renee Palmer steps forward, and the woman standing before the television cameras is the mysterious person who rescued Liam and Augur from the apartment.

At Augur's apartment, Holo Lili tells him that the destructive code which erased her operating system was a Trojan file, version, PK_2300.EXE. She has purged the infected patches and is ready to reinstall her programmes using the master disks. Augur asks Liam how it is possible that there an be no data on this woman, and Liam says that Renee Palmer knew they were coming. Augur says that Renee cannot keep a low profile forever. Holo Lili says that once her systems are up and running again, she will start scrolling. Augur looks pained and tells her that it won't be necessary. Holo Lili says that she has just installed a great new masking programme and asks Augur if something is wrong. He says that everything is fine, but she doesn't believe him. Augur tells her that they need to have a talk, and that he is retiring her program. Holo Lili protests; she is fully functional, and if he needs to upgrade her operating system...... She asks Augur again what she has done. He tells her that she hasn't done anything wrong, but that the real Lili is dead. Holo Lili is distraught and says that if the real Lili doesn't exist, then she doesn't exist and vice versa. The tearful Augur says that her death will be painless and presses the Delete button on his console, as Holo Lili pleads with him not to.

Lili Marquette, looking pale but unhurt, is standing near a port hole on the mother ship gazing out. An unseen voice tells her that it is time to go. Lili turns, looking frightened.