Lex has been secretly trying to turn Wes Keenan, a military man who supposedly died fighting in Afghanistan, into a "super-soldier" by injecting him with DNA pulled from the various meteor freaks he has captured. After a crooked senator threatens to expose his secret labs, Lex dispatches Wes to kill the senator, but Lois witnesses the attack and inadvertently becomes the super-soldier's next target. Clark asks Lana for any information she might know about Lex's project.
→ see also Category:Screencaps from episode 6x21
Lex and his assistant Bartlett are summoned to his laboratory located underneath Reeves Dam, where the doctor in charge reports that sections of the laboratory are becoming compromised systematically. The dozens of guards are being completely defeated as an unknown threat grows closer. As Bartlett and the doctor panic, the door bursts open. Lex fires, but the bullets are absorbed by a forcefield. A man emerges from the forcefield and levels a gun at Lex's face. It is Wes Keenan, but instead of shooting, he stops and waits for further instruction. Lex times his arrival and is pleased with his response time. He gleefully declares the test run a success and orders the doctor to set up new guards so he can do it again.
Back at the Luthor Mansion, Lex finds Lana arranging flowers. He hovers over her since she was recently shot. Senator Burke arrives and Lana remarks that he has been seeing a lot of the Senator as she leaves. Burke asks for an update on Project Ares and Lex reports that everything is on schedule. Burke reveals that in fact, everything is ahead of schedule; he knows that Lex has already started mass-production. He got the military to cooperate with the Project, but now intends to shut it down because the Senate will find out the Project's true mission. Lex points out all the money he's paid Burke for his cooperation. Burke threatens to scrutinize all of LuthorCorp's business deals for the last twenty years if Lex exposes his role in the Project. It is revealed that Lana listened in on the entire conversation.
Lionel is viewing the Patagonia tourist video of the escaped Phantom Zone wraith and jotting down Kryptonian symbols. Clark storms into his office and Lionel puts everything away. Clark begins to question him about his role in Lana's marrying Lex, telling him that Lana intended to leave Lex. He thinks Lionel threatened Lana, but Lionel just said Lana changed her mind. Clark is still suspicious.
Lois is trying to console Chloe at the Talon, who is depressed over Jimmy's departure. Clark arrives and Lois exits, saying she has to chase a lead on a dirty senator. Clark asks Chloe what's up, but Chloe says Lois hasn't told her much about the story. Clark tells Chloe that he went to see Lionel, but he didn't say anything, just like Chloe. He tells Chloe that Lex is capable of anything and urges her to tell him why Lana went through with it, even reminding Chloe what Lex did to her and her mother. This upsets Chloe even more; she says that Lana must have a damn good reason for staying in the marriage.
Lois is in an alleyway, bribing a waiter at Burke's favorite restaurant. With his tip, she is able to accost Burke just as his limo pulls up. She starts to question him about his Cayman accounts but he blows her off. He tells his guards to get her out of here but an unseen assailant suddenly appears and kills Burke and his men. He advances on Lois, but she recognizes him and calls out his name. He hesitates, then disappears by turning invisible and super-speeding away.
Chloe and Lois meet Clark at the Daily Planet. The papers reported that Burke was killed by the Mob, but Lois tells Clark that she saw the culprit—they grew up together as Army brats. She insists that Wes was a model soldier. Chloe reports that Wes Keenan was killed in action, but Lois stands by her story. The rest of Wes' records have been classified.
Wes is back at the laboratory being monitored by the doctor when Bartlett announces there was a witness. Lex instructs the men to take care of it and they prepare Wes for programming.
Clark and Martha tell Lois that it will be safer for her to stay at the farm and Lois asks Martha to use her government connections to get the rest of Wes' records. Martha promises to do what she can. When she leaves the barn, Clark warns Lois not to get in over her head. Lois says that she and Wes were close and she has to find out what happened to him. They hear a strange noise and Wes appears out of thin air. He throws Clark across the room and prepares to stab Lois. Clark recovers just in time to see Wes grab Lois and disappear. He goes to get Chloe and tells her that when Wes hit him, it felt like his battle against Titan. Chloe says she hasn't gotten his file yet, but she discovered that Wes' wife was Jodi, the woman who tried to kill Lex in the tunnels. They realize that Wes is connected to Lex's Level 33.1 experiments somehow. Clark asks Chloe to contact Oliver Queen and his team for information while he goes to talk to Lex. Chloe doubts that he will tell him anything so Clark decides to talk to Lana instead.
Lana is getting ready for bed when she finds the bedroom filled with candles. Lex admits he was trying to set the mood and is disappointed when Lana pulls away. Their moment is interrupted by Bartlett, who reports that "the asset failed to return." Lex leaves in a hurry and Lana hears Clark whisper her name.
Clark appears behind her and says he needs information because Lois is in trouble. Lana tells him about Project Ares and suggests he talk to Senator Burke, but Clark informs her that Burke is dead. Lana also says that Lex just learned about an "asset" failing to return and Clark is sure it is Wes. He warns Lana about Lex, but Lana just says people keep secrets to protect their loved ones. Clark speeds away just as Lex returns to say he has to go into the office.
Lex storms into the laboratory and berates the doctor for losing the subject. The doctor says Wes is impossible to track, but activates LuthorCorp satellites in an attempt to track Wes down and re-initiate his commands.
Lois wakes up in a warehouse with Wes standing over her. He is reciting programming jargon like a robot and Lois attempts to get through to him by recounting a story in which they got drunk in a warehouse as children. She realizes they are in the same warehouse and pleads with Wes to remember her. Wes comes to his senses and explains to Lois that he was stationed in Afghanistan, but he was badly injured. Lex offered him the opportunity to help soldiers protect themselves and he agreed to be part of the project. Lois assures him that they will expose the Project, but Wes begins to fall back under Lex's command. He urges Lois to run.
Clark and Chloe meet up at the farm. He tells her that Lex is building super-soldiers, and she reveals that Oliver's team encountered an earlier model that had an extremely powerful forcefield. Martha has been able to procure Wes' file. Chloe speculates that since Wes' programming is failing, that he'd go back to a familiar place. They realize that Wes and Lois grew up at nearby Ford Addleson and Clark speeds away.
Lois is trying to find a way out of the warehouse, but Wes has now fully succumbed to the mind control. He chokes her unconscious, but Clark catches her and moves her out of harm's way. Wes throws Clark across the warehouse and prepares to attack him. Suddenly, he appears to Clark´s eyes although he is still out of his reach. It seals his fate because Clark has enough time to use his heat vision at maximum to blast away the forcefield and knock Wes out. Lois awakens and runs to Wes' side. She assures him that he will be fine, but he tells her that he would rather die than be controlled by Lex. Lois begins to cry as he dies. Unseen, Clark watches the two with sadness and regret.
Clark is disappointed that nothing can be done about the exploitation that Wes suffered and asks Martha if there is anything she can do. Martha says she has little influence, but just then, Lionel arrives to announce that he suggested Martha as a replacement for Burke in the U.S. Senate until the next election. Clark agrees and says that Jonathan would have wanted her to and she has the potential to really make a change.
Lex is on the phone, demanding that Wes' body be transported back to the lab. Lana asks him why he didn't come home and Lex casually says that there were complications with Project Ares. Lana feigns ignorance and Lex is annoyed. He reveals that he knows Lana listened to his and Burke's conversation. Lana just says she was curious and Lex tells her that all she had to do was ask.
Clark tells Chloe about Martha's future plans and they wonder if Lionel has ulterior motives, but both agree that Lex is a bigger problem. Chloe is optimistic that Lois will tell the Feds everything and Lex will be punished, but Lois arrives to tell them that Wes' body disappeared. She vows that Lex will pay for what he did and storms away.
Lex orders a complete study on Wes' corpse, but the doctor reveals that they do not have any more alien DNA from Titan to continue the project. Lex is undeterred and reveals that he already is working on securing a replacement source and that he has hundreds of subjects ready to be turned into super-soldiers.
- Tom Welling as Clark Kent
- Kristin Kreuk as Lana Lang
- Michael Rosenbaum as Lex Luthor
- Erica Durance as Lois Lane
- Allison Mack as Chloe Sullivan
- John Glover as Lionel Luthor
- Annette O'Toole as Martha Kent
- Tahmoh Penikett as Wes Keenan
- Gerard Plunkett as Dr. Donovan Jamison
- Alan C. Peterson as Senator Ed Burke
- Ben Ayres as Jason Bartlett
- Gino Cocomello as Waiter
- "Is This Where" - Julie Gribble
- A "prototype" is the original model on which something is based or formed.
- The title refers to Wes Keenan, the "prototype" of Lex's super-soldiers.
- Antagonist: Lex Luthor.
- Clark’s Abilities: Invulnerability, Super-Speed, Heat Vision, X-Ray Vision (attempted), Multi-spectrum Vision (possibly)
- This episode was shot 20th, but was shown as the 21st episode of the season. 
- Despite claims to the contrary in previous episodes, we learn that Lionel can indeed read Kryptonian. 
In Other Media
- As Clark pointed out, Ares is indeed the Greek god of war (or more specifically, bloodlust). Ares is also a supervillan in DC comics and the archenemy of Wonder Woman.
- Clark says he can lease the back 40 acres to Ben Hubbard to cover finances. Hubbard is a character from the Superman: The Movie and Superman Returns who took over the Kent farm and cared for Martha when Clark left for Metropolis.
- Tahmoh Penikett, who played Wes Keenan, also played Vince Davis in Resurrection.
- According to TV.com, this is the lowest rated episode of the series. 
- Tahmoh Penikett appears in Man of Steel as Jed Eubanks, an Arctic worker interviewed by Lois Lane. Penikett is one of several actors (including Amy Adams, Alessandro Juliani and Ted Whittall) appearing in both the universes of Smallville and the DC Extended Universe.
- Penikett is one of three actors to have screen time with Lois Lane in both universes, along with Michael Cassidy and Alessandro Juliani.
- Clark and Chloe discover that Wes Keenan was the husband of Jodi Keenan, who was in Nemesis.
- Clark mentions leasing out the "Back 40". This area of land on the Kent farm was previously referenced in Lockdown when Jonathan Kent sold it to repay Lionel Luthor's contribution to his state senate campaign. Lionel then refused to accept the payment after Jonathan's death and returned the land to the Kents after Clark saves Lionel's life in Vengeance.
- Dr. Donovan Jamison had previously appeared in Chloe Chronicles, Chloe Chronicles, Volume Two (both times played by Gerard Plunkett), the Smallville comic book story Exploit, and the animated comic Justice & Doom. This is the first time he's ever appeared in a normal Smallville episode.
- In Burke's conversation with Lex, he revealed he had one of his men investigate Lex's organization for a mole, but that Burke's man was killed by gunshot before he could reveal anything to Burke. This may allude to the unnamed gunman in the previous episode, Noir. If so, it would indicate the gunman acted on his own initiative to try to kill Lana or had been ordered by Burke to kill the mole before reporting back to him. It's likely either Lex or Lionel then had the gunman killed either to avenge Lana or keep the gunman from reporting back to Burke (or for both reasons).
- When discussing Wes' powers, Chloe mentions Clark's teleporting girlfriend Alicia Baker (Obsession, Unsafe, Pariah) and Clark mentions Graham Garrett, who could become invisible (Fade). He also appears to have Bart Allen's super speed (Run, Justice), the Twins' forcefield ability (Mortal) and Titan's strength (Combat).
- This was the first time since season 5 episode Mortal that Alicia Baker has been mentioned.
- Clark remarks that Lois can stay with them on the farm like when she first came to Smallville, which occurred in the fourth season. Lois moved in with the Kents in Façade, then again in Recruit.
- Lois jokes that Clark wants to catch her in the shower again. However, Lois' memory is slightly inaccurate. She actually intruded on Clark's shower in Gone. Lois could also be referring to a scene in Fade in which Clark sees her in the nude after coming out of the shower. This was however not at the Kent Farm, but when Lois resided at the Talon apartment.
- Chloe references an Ares prototype like Wes which required something resembling a miniature nuclear explosion to subdue. These events take place in Justice and Doom episode four, where Ollie's Justice League battles the prototype.
- Jason Bartlett, the Project Ares supervisor, also appeared in Combat, Nemesis, Noir, and Phantom.
- Chloe mentions Sam Lane, who appeared in Season 4's Gone and Facade.
- This episode marks the 57th appearance of Clark's red jacket & blue shirt outfit, which he wears frequently throughout the series.
- Chloe's "Mrs. Kent goes to Washington" comment and her comparison of Martha to Jimmy Stewart is a reference to Stewart's 1939 movie Mr. Smith Goes to Washington, in which Stewart's character Mr. Smith is a hopeful, idealistic newly elected senator, but is disappointed to discover rampant corruption and scandal.
- Lionel: It's surprising, Clark, what people will do when they, uh, feel they have no other options.
- Clark: If I find out that you had anything to do with Lana marrying Lex, the gloves will come off. How do you like that option?
- Lois: Besides, distance is good for the relationship. That is what all the guys who have moved away from me have said.
- Clark: Lana, whatever reason you had to go through with the wedding, it was the wrong choice. You have no idea what he's capable of.
- Lana: You'd be surprised what I know.
- Clark: Then why are you still here?
- Lana: We all have our secrets, Clark. Sometimes we have to keep them to protect the people we care about.
- Clark: You and Dad always taught me to put other people first, to use my abilities to help those in need. You have the chance to affect so many people, to change so many lives if you go to Washington. That's where you need to be if you want to make a difference, Mom. And that's where people like Wes need you to be.
- Lana: Lex, I'm sorry. There is no excuse. My curiosity got the best of me.
- Lex: You're not a cat, Lana. Don't skulk around like one.
- Lana: It won't happen again.
- Lex: Every time I open my heart to someone I care about, I've ended up being very disappointed. If... if you ever betrayed me, I don't know what I'd do.
- Lana: I'd never hurt the man I love.
- Wes Keenan (to Lois): Don´t let them do this to anyone else. Okay?
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