James begins his day not particularly excited about the prospect of going to work. Before he leaves, he listens to a phone message left by his twin sister, Jessica, who informs him that she’s coming to Cleveland to do research for her new movie, Slayer Wars, in which she has the lead. She tells James that she wants the two of them to talk, but it’s clear that James is not looking forward to seeing his estranged sister.
Once at work, Anya reprimands James for not using his time more wisely. He’s doing things he shouldn’t be doing (like fixing the Slayer comm system) and then not doing what he’s supposed to be doing (like keeping his appointments with Giles). When James complains that his hard work is unappreciated, Anya tells him that his work stopped being hard a long time ago and that he should take some initiative and show the Council what he’s capable of. James seems to consider this idea deeply.
Later that night, a man is seen exiting the underground lab of Dayson Laboratory, having knocked out a scientist and taken his security card as well as a data rod containing the scientist’s research. The man appears to be James, but in reality he’s James’s Clone, who was created illegally in the Dayson Lab.
The next morning, Jo and Katie are in bed, enjoying some quality time together on their last day off before having to report back to work after their two-week detention for illegal magic use. Katie tells Jo about a dream she had, in which they were at the beach with friends and it began to rain. Katie also reminds Jo about the errand she has to run later. Jo whines at the prospect of Katie leaving until Katie promises that after she returns, they’ll have the rest of the day to do whatever they want.
When James arrives at work, he finds Katie in the Council lobby. He cheerfully welcomes her back, but she soon notices his somber mood. He tells her about his sister’s impending visit and their tumultuous relationship over the years. Katie encourages James to forgive and forget, but James just frowns in response.
Katie’s errand is a meeting with Giles, who welcomes her back and then asks for her help with Jo, who is still refusing to speak to him. Katie says that she’ll talk to Jo, but she can’t make any promises. Giles thanks her and then updates her on her former watcher, Sean Rayne. He has recovered from his injuries and is scheduled to be transferred to an off-site holding facility. Tyrell, however, is set to remain in the Council’s detention area for the time being.
Back at Jo’s apartment, Katie reports her visit with Giles and eventually convinces Jo to talk to Giles. Jo admits that it’s important to get everything out in the open and talk about it. Katie becomes somewhat rattled at the idea of sharing all, but doesn’t reveal anything about her secret.
In the Computer Center, Anya comes in to find a clearly nervous James (who is actually the Clone). She asks him what he’s been up to. When he admits that he has not been working on the Slayer comm system, she praises him for following her advice. The Clone leaves, citing a supposed appointment.
On her way to see Giles, Jo stops in her office to check her email. While there, she discovers that no one accessed Willowgram while she and Katie were in detention. Concerned about the well-being of the program, Jo determines to ask the Council to recognize Willow as semi-sentient and to grant her certain rights. When Jo goes to see Giles, she skips any amenities and jumps directly into her request for Willowgram. Giles does not share Jo’s views, and the two end up fighting about the issue as well as about Giles’s reaction to Jo and Katie’s magic use.
Later, James is stuck participating in the official welcome for his sister, Jessica, who is a famous TV and movie star. James arrives with Lex and Toni, and they join Velika Petrova, Livia, and John West. When Jessica gets there, she quickly wins over all but James, who greets her very coldly. She gives him the card to her hotel and expresses hope that they can get together and catch up. Jessica leaves with Velika and Livia to tour Slayer Command.
Back in Jo’s apartment, Katie entertains herself by looking at Jo’s old books. In the process, she discovers an old photo of Tara Maclay. Seeing the mirror image of herself, Katie freaks and flees the apartment. Jo comes home and finds that Katie has gone and has left a flimsy excuse about something coming up at Slayer Command.
Giles comes across the Clone in the hallway near Slayer Command. Thinking the Clone is James, Giles reminds him that the two of them still need to meet later on. The Clone emphatically agrees, and Giles goes on his way.
Later, James is working on the Slayer comm system when Anya interrupts, chiding him for not having his link on. Then she scolds him for working on the Slayer comm system when he said earlier he wasn’t going to. James looks confused, but shakes it off and asks Anya why she’s there. She tells him that Jessica is coming to tour the Computer Center, so he needs to get there right away.
Meanwhile, Giles has a meeting with his friend and colleague, Veronica Wyndam-Pryce, who gives him her opinion on how he’s done as Chair for the last two weeks. She expresses surprise at his handling of Jo and Katie’s magic use. Giles admits it was a difficult decision, and he felt torn between the Council and Jo. He fears that he has totally alienated himself from Jo and reports that she’s now also mad at him because of his stance on the Willowgram issue. When Giles explains, Veronica encourages him to consider accepting Jo’s proposal for the computer program. She tells him that the Council needs the fearless, radical Giles, not the Giles who’s worried about what the Council thinks of him.
When Jessica and Livia arrive at the Computer Center, James still doesn’t warm up to his sister and takes her on a very short and cold tour. Anya intervenes and livens up the visit. When Jessica thanks Anya, the android takes it upon herself to give the actress a tour of the Council Hangar, and Livia is forced to trail behind.
Giles goes to Jo’s apartment, and she reluctantly lets him in. He tells her that he’s decided to take the Willowgram issue before the Council, but he needs her to prepare the detailed proposal and to bring it and the Willowgram to the Council meeting that evening. Jo happily agrees. Though getting along better, the two have an awkward parting.
Meanwhile, Katie begins researching the life of Tara Maclay, but is disappointed to find that there is very little information available on her. When Jo calls, Katie decides not to answer the phone.
At the Council meeting, Giles and Jocasta present their case for securing certain rights for Willowgram, namely the following: that she be given full access to both the Council databases and the worldwide data network grid, that her programming be rerouted directly to Jo’s office, and that she be given complete control of her own access protocols. Despite objections from Travers, the motion passes.
Before the night is over, John West meets a person who appears to be James in the elevator on the detention level floor. The man seems evasive in his conversation, but it isn’t clear whether it’s James or his Clone.
The next morning, James finally meets with Giles. James admits he hasn’t been pulling his weight, and he assures Giles that he’s ready to take on more responsibility, which Giles promptly gives him in the form of two assignments: handling the technical aspects of the Willowgram ruling and investigating the mysterious break-in at Dayson Laboratory. When James gets to the Computer Center, Anya is on her way out, determined to find Jessica so that she can continue enlightening the actress on the ins and outs of Council operations.
Later, Toni comes through the lobby carrying a large bag of snacks. When she sees the Clone, she thinks that he’s James. She tells him he’s invited to an impromptu picnic and immediately drags him out the front entrance.
At a nearby park, the new Scooby gang gathers for a celebratory picnic in honor of Willowgram’s new status and of Jessica’s visit. Attending are Giles, Jo, Katie, Lex, Toni, Anya, Willowgram, the Clone (who everyone thinks is James), Livia, and Jessica. Fun is had by all, and even the Clone and Jessica seem to be getting along. The fun is interrupted when Giles gets a call that Rayne has escaped, the transport carrying him having never made it to the off-site holding facility. Everyone heads back to Council HQ.
Giles, Jo, and Katie go to the detention area to speak with Tyrell, only to find that he also is missing, having been transferred with Rayne at the last minute. When Giles demands to know who authorized the transfer, the nervous guard says the transfer was signed by Giles himself.
In Jo’s conference room, the group anxiously awaits James’s arrival to the scheduled emergency meeting. Giles finally calls James, who shows total surprise at the news that Tyrell and Rayne are missing. Giles impatiently orders James to get there right away. When James finally arrives (sans Anya, who is mapping Willowgram’s rerouting), the group shares what they’ve learned. Someone used Giles’s clearance to get Tyrell transferred with Rayne. On the way to the holding facility, the transport carrying them disappeared, and there’s been no sign of them. Giles orders Lex and Toni to investigate the transport angle, he tells Livia and Katie to get the Slayers searching, and he instructs Jo and Willow to research the transfer records. James offers to help, but Giles tells him that he needs to continue the Dayson investigation. After the meeting breaks up, Katie mentions to James that she was glad to see him and his sister getting along earlier. Before the confused James can say anything in response, Katie has to leave.
James returns to the Computer Center and researches Dayson Laboratory. He discovers it’s a Council-sponsored medical research lab and cloning facility. Unable to discover what is being researched, James and Anya go to the facility in person. There, they meet with the administrator, Dr. Carilyn Byrne, who reluctantly tells them about the break-in. She says that an intruder broke into the lab of Dr. Martin So, attacked him, and stole his security card and a data rod containing his research on nano-technology and its use in fighting viruses. She tells them that she suspects a rival research group. When asked if they can see Dr. So or his lab, she politely refuses, saying that Dr. So is in a coma and that the lab hasn’t been cleared by haz-mat. James and Anya return to the Council, where James does some serious hacking into Dayson’s databanks.
Meanwhile, Toni meets up with the Clone in the hallway and asks him if he can arrange for his sister, Jessica, to get her picture taken with her. Not knowing what else to do, the Clone agrees, and Toni skips happily away.
When Giles goes before the Council to break the news about Tyrell and Rayne’s escape, he comes under fire since his name was on Tyrell’s transfer order. As a result, Travers is elected to oversee the investigation into the escape.
Giles calls the gang together to share what they’ve learned so far. Lex and Livia report that the transport that had been carrying Tyrell and Rayne was found in Lake Erie, but there is no sign of the escapees. Jo explains that the transfer request came from a shadow account designed to mimic Giles’s, but she’s had no luck in tracing it further. James shares what he’s learned about the Dayson case. It wasn’t a break-in, it was a break-out. An illegal clone (whose identity is as yet unknown) broke out, taking along Dr. So’s security card and research data. The Dayson people are extremely worried about finding the clone, afraid that their entire operation may be compromised. They are particularly concerned about James and intend to send an operative to the Council right away. The gang speculates that the purpose of the operative is to keep an eye on James since he’s the investigator or to watch out for the clone, who may be intending to turn over the data rod and expose their operation.
When the meeting breaks up, Toni walks to the elevator with James, Lex, and Livia. She mentions her photo request to James, who has no idea what she’s talking about. When the elevator door opens, the Clone is revealed. Everyone is in shock as they see two Jameses before them.
The Clone quickly closes the elevator door and escapes. Livia runs for the stairwell, and Lex initiates a building lock-down.
A few moments later, the gang reconvenes in the conference room (minus Livia, who is still searching for the Clone). Although James admits that he complied with the Council’s DNA sample requirement when he was hired, he denies ever giving any permission for cloning. The gang once again speculates that the Clone is there to turn over the data rod. James vehemently disagrees, believing instead that the Clone is an assassin sent to kill him and take his place. He wants the Clone not simply detained, but destroyed. Giles issues an intruder alert but instructs James to stay put in the Computer Center so that he won’t complicate the search.
Meanwhile, Jessica has gotten herself lost near the Computer Center. She runs into James, and they have a big argument, rehashing old rivalries. When James announces that he doesn’t have time to fight with her because there’s a Clone running around pretending to be him, Jessica is surprised. She wonders why their parents activated one of James’s clones. James doesn’t know what his sister is talking about. Jessica explains that their parents ordered clones for both of them without their knowledge. Jessica says that she found out when she had to have her kidneys replaced last year—a surgery James was completely unaware of due to their estrangement. James figures that his fugitive Clone has nothing to do with what his parents had done and assures Jessica that the Clone will be taken care of. Jessica is appalled to learn that James wants the Clone destroyed. Legal or not, the Clone is a person who doesn’t deserve to be killed, she argues. Suddenly, she realizes that the person she was getting along with so well at the picnic wasn’t James at all. They both accuse each other of being cold and callous until James finally stomps off.
Meanwhile, Jo and Katie help research on the computer, with Jo working on the Tyrell/Rayne escape and Katie digging into the Dayson files. Katie mentions that the cloning thing is weird to her; she’s uncomfortable with the concept of knowing that there’s "another you" out there. Jocasta says that it’s no stranger than knowing you’re reincarnated. Katie agrees, but looks away with a frown, clearly thinking of her earlier discovery of Tara’s picture.
James attempts to work in the Computer Center, but soon grows frustrated. He appears to come to some decision, then rushes out. On his way to the elevator, he runs into his Clone. James and his Clone argue over whose life is whose, and then the two get into a scuffle.
Jessica has decided to try again with James and has returned to the Computer Center. When she exits the elevator, she finds James wrestling on the floor with the Clone. She freezes, unsure about what to do. Livia emerges from the stairwell, stun gun in hand. But the slayer doesn’t know who’s who. She asks Jessica who the real James is, but Jessica doesn’t know. When the Clone appeals to Jessica and plays on their family ties, Jessica knows he’s not James. Jessica informs Livia who the Clone is, and Livia stuns him. When James asks Jessica how she knew who was who, Jessica says sadly, "You never would have said ‘we’re family’."
Later that night, Jo and Katie are having supper. Katie is clearly preoccupied. Jo presses her for details. Katie tells her about finding the photo of Tara, but says nothing about her secret.
The next morning, Giles goes before the Council to determine what should be done about the Clone and the illegal facility he came from. James has since changed his mind about the Clone and doesn’t want him destroyed. However, Giles is unable to prevent Travers from convincing the Council to take drastic measures. The facility is to be shut down, all legitimate medical research and services are to be transferred to another lab, and all unauthorized work is to be completely classified. In addition, all illegally stored DNA and its derivatives, including all clones, those activated and those in development or in stasis, are to be destroyed. James is upset by the news and storms away. Jo tries to comfort Giles.
Travers is shown conversing with Tyrell via videophone regarding the Dayson affair. Travers assures Tyrell that the matter has been taken care of, although he is forced to admit that the data rod that the Clone stole has not been recovered.
An upset James returns to his office, where he tries to call Jessica at her hotel. Unfortunately, she has already checked out. James takes off from work and goes home, where he finds a package whose contents surprise him.
Meanwhile, Jo and Katie and Giles are outside Council HQ making their end-of-the-day good-byes. Unknown to them, they are being watched by Sean Rayne, who smirks and says, "Be seeing you."