Back on the mothership, a Volunteer informs Sandoval that she's taken care of his "problem," whatever that is.

Sandoval then goes to tell Zo'or he's ordered a team up from Earth to repair the damage to the ship. Once again, the Taelon leader informs him this will not be necessary -- the mothership is an organic construct capable of regenerating to heal the damage. The pair then turn their attention to the matter of Lili Marquette. Sandoval orders her brought to the bridge, but is informed that this is not permissible.

Lili Marquette in space
Meanwhile, Liam and Augur try to uncover the identity of their mysterious savior, only to be interrupted by a news report announcing Lili's sabotage of the mothership and her death in the subsequent explosion. Enraged, Augur begins tearing the room apart, but Liam manages to calm him down.

Later, in the office of the North American Companion, a furious Liam confronts Da'an about Lili's death. As it turns out, the Taelon is equally upset, viewing any attack against his race as an assault on the Commonality. While Liam blames Zo'or for making Lili's actions necessary, Da'an lays the blame at President Thompson's feet. Liam retorts that Thompson is Zo'or's puppet, and storms out, vowing to prove that the Resistance didn't engineer the assassination attempt.

As Volunteers prepare to dispose of Lili's body, Liam breaks in and tells them he's taking the corpse back to Earth. Although Sandoval informs him that Lili's treasonous actions toward the Taelons make this impossible, Liam still pleads with the Taelons' elite bodyguard to give him the body and look the other way. Sandoval refuses. The body is committed to space.

An unguarded bit of protein
Sandoval then revisits the site of the abortive assassination attempt on President Thompson, where he assures Hubble Urich, Thompson's chief of staff, that the FBI has conclusive evidence of the shooter's identity but is waiting for the Washington medical examiner, Bob Anders, to corroborate their findings.

Urich departs and Anders arrives. He notes that the forensic evidence indicates the assassin stood on a catwalk, and his skrill-killed remains landed on a seat at ground level. He then wonders why the FBI needs his findings since they already have all this evidence. Sandoval explains that since this was an attack on the President, he wants to cover all bases, and orders Anders to report his findings to him before going public. After dismissing the forensics expert, Sandoval nods significantly to his aide, Tate, who immediately slinks away.

Anders, apparently a popular figure in Washington social circles, then gets a visit from Liam. Anders bemoans the impact of Taelon technology on the science of forensics, explaining to Kincaid that between the FBI and Sandoval's skrill, there isn't much evidence left. After ingenuously placing the DNA sample harvested from the crime scene in a cooler, he then walks away, leaving Liam free to liberate the sample.

Back at the hideout, Liam and Augur take a break to share their feelings about Lili's death before Augur scans the stolen DNA sample. Their worst fears seem confirmed -- the scan identifies the material as belonging to a Resistance member named Albert Phillips. Liam refuses to believe it and sends Augur out to find people who know Phillips.

Sandoval orders Tate to "take care of" Anders.

Liam meets with Emily Langford, a friend of Albert Phillips. She informs him he was captured by the Taelons weeks ago, and refuses to believe that Phillips, a pacifist, could have made the attempt on Thompson's life.

Liam then gets a call from Anders, who compliments him on stealing a sample from under the nose of the FBI. Anders reveals that he doesn't trust Sandoval, and offers to tell Liam the real facts of the case. Warning Anders to be careful, Liam sets out for the examiner's office, but it's too late -- Tate emerges in the office and strangles Anders to death. When Liam arrives, an inconclusive firefight breaks out, but Tate escapes anyway.

Urich informs Thompson of his concerns regarding the state of emergency. The President assures him it is a temporary measure, but his chief of staff suggests that Thompson should stand up to the Taelons before it is too late.

Apparently at a loss for fresh leads, Liam and Augur again contemplate the mystery woman who saved them at the beginning of the episode, but shrug off the speculation to get back to work. After Augur performs a dating analysis on Phillips' DNA sample, they learn it is over a month old, which rules out Phillips as an actual suspect. Could Sandoval be trying to clean up after the real assassin?

Augur wonders whether the real assassin's DNA might still be "molecular-bonded" to the floor of the catwalk, fused into the metal after getting blasted by Sandoval's skrill. Unfortunately, Tate has a similar thought, and so Sandoval's sinister henchman rushes to the scene to plant a bomb to take care of the evidence and Liam -- who shows up to scrape some genetic material off the floor -- as well.

Sandoval, I accuse you!
As luck would have it, Liam manages to get the sample and escape the bomb in the nick of time. Needless to say, it has degraded somewhat, but Augur manages to run a scan on the DNA sample, and is shocked to learn that the real assassin is none other than Judson Corr, the man Sandoval hired to murder William Boone's wife.

Liam provides Urich with this new puzzling evidence. Urich wants to know why Liam is telling him this, but all Liam can say is that he's looking forward to President Thompson's speech. Urich understandably wants more evidence before doing anything.

Augur's computers find a match for the mystery woman, but she's been watching him and, saying she's impressed that he found her ahead of schedule, she uploads a virus into Augur's network that crashes his system. Augur falls in love.

With time running out for what's left of the Resistance, Liam and Augur return to Anders' lab. Luckily, Tate didn't look for backup copies of the DNA evidence, so the two heroes easily find enough new data to wrangle a presidential audience.

On the mothership, Zo'or and Sandoval watch as President Thompson announces that he has evidence suggesting the Resistance didn't engineer the attack on his life. He rescinds the state of emergency and orders the release of all prisoners held aboard the mothership. Furious, Zo'or dispatches Sandoval to fetch the President.

Liam meets with Da'an and tells him that Sandoval, acting on orders from Zo'or, engineered the attack. Liam then goes to supervise the return of the Taelons' prisoners.

Keep the balls in the air
Zo'or and Thompson exchange angry words. Zo'or admits to having Thompson shot in order to keep Jonathan Doors from becoming president.

Understandably, once Thompson gets back, he forbids the Volunteers to continue their attacks against the Resistance.

Urich suggests it might be time for the President and the Taelons to redefine their relationship, while Zo'or and Sandoval do some redefining of their own by reminding Thompson that they almost killed him once before and might do so again.

As the prisoners go free, Liam meets Jonathan Doors and, in an effort to make peace, informs him of Lili's death. However, Doors tells Liam he has made a deal of his own -- as Liam watches in shock, Zo'or arrives and tells Doors he "looks forward" to their new association.

Zo'or and Doors then hold a joint press conference to announce their alliance. When Doors explains that working with the Taelons is in the best interest of humanity, Da'an, Liam and Sandoval all seem disturbed. Doors dedicates his company to developing consumer applications for Taelon technology, and introduces the Doors Industries executive in charge of this effort. She is Renee Palmer, the mystery woman who saved Augur and Liam earlier.

Back in his lair, a grieving Augur makes his peace with Lili's memory by then retiring the virtual Lili's program.

On the mothership, a woman dressed in black stands in the shadows. It's Lili! A female voice tells her, "Time to go, Captain Marquette."