The episode begins with Jo organizing a memorial service for Holly. Jack and Jo are informed while organizing the memorial that, a new security system is being set up at the facility. John tells the guys who are installing the security system to install it somewhere else in the facility, for the time being. Henry then says a few words at Holly’s memorial service. Douglas though turns down the offer to give a eulogy, much to everyone’s surprise. Later Jack volunteers to let Henry experiment on him, for something to do with what happened to them in the Matrix. Jo meanwhile tells Zane that she is worried about Douglas as he has been missing meetings, and not really concentrating on his work.
Zane is then informed much to his horror that, everything to do with the Astraes is going to be impounded by the DOD. Which would mean the Matrix computer would be too. Douglas in the meanwhile is with Holly in the Matrix. He tells Holly about the memorial service held in her honor. Zane suddenly pulls Douglas out of the Matrix and tells him about the DOD’s plan. The officials from DOD come in to confiscate the computer, and Doug tries stopping them. The official tells him that the computer is a security threat. He is then taken out by Allison and Jo. He then tells them that Holly is inside the computer. Allison later tells Jo that they should Douglas. Henry meanwhile begins his experiment on Jack, and it doesn’t go as well as expected. Zane meanwhile copies all the files from the Matrix computer, before it’s impounded. The DOD official then tells Jo how the new security system would work. Zane later tells Doug that he has transferred Holly’s character file into his computer from the Matrix computer. Zane then finds out much to his dismay that the partition which he copied was empty, which means Holly is still on the impounded computer.
Henry and Jack meanwhile find out that, Jack is able to move a robotic arm with his mind. Then suddenly it seems the arm grows a mind of its own and begins banging the glass casing it’s kept in. Henry somehow manages to subdue the arm by cutting the power supply. Allison meanwhile tells Doug to come clean about Holly, so Holly can be studied and he can be helped. Doug doesn’t agree and feels that, if the truth comes out Holly will be dissected. Zane comes in and tells Doug and Allison that the DOD would be formatting the computer thus deleting Holly, before it’s shipped out. Allison then tells them that there might be a way to get past the DOD security system and access the computer. Doug then crawls through the ventilation system to bypass the security system. The DOD official meanwhile activates the security system. Suddenly the security system goes offline, and before it does, on the screen is seen a moving hand. Zane and Allison too experience this, but Zane tells her it wasn’t him. Allison then informs Doug that the security system is offline, and hence he has a few minutes to salvage Holly. Doug then reaches the place where the computer is stored. He in there begins hearing voices, and then sees all the lights in place blow out. The whole place is then completely dark, and Dough is completely terrified after all that has transpired.
Doug then finds the computer and proceeds to copy the data onto a flash drive. The security system meanwhile comes back up. The security alarm then goes off immediately. The DOD official and Jo then see on the screen what Doug is doing. Doug meanwhile tells Zane “nothing is happening” and goes into the system. Inside he searches for Holly. Later, Doug returns. He has discovered that the data in the machine has already been deleted. He is then placed under arrest by the DOD officials. Later Jo tells Jack about the strange things that are happening all over the facility. Later Allison tries talking to Jo and explaining to her Doug’s predicament. Jo on the other hand feels that they should all help Doug forget Holly. Later Jack tells Henry that things were going wrong all over the facility, so it might not have been him who was the cause for the robotic arm to behave weirdly. Suddenly a laser device which has been erected in Holly’s memory begins to attack Jack and Henry. They somehow manage to escape. Henry then observes that the signs left by laser aren’t random. Zane meanwhile finds a ghost like program in the security mainframe. The DOD official then activates an antivirus to kill whatever is there in the system. Henry meanwhile tells Jack that all the weird things that are happening might be someone trying to communicate with them.
They along with Doug and Jo then see the trail created by the laser, and from a height it reads “Help me”. Doug then tells them that Holly did not stay in the computer program because she has a mind of her own, and is alive. The antivirus in the meanwhile is going to process with the system purge in 3 minutes. Zane tells Jack and Allison “if the purge gets to Holly she is gone for good”. The only resort left is for Zane to find Holly and hack her, an escape route. For this they have to stay one step ahead of the purge. Jo then tells the DOD official to stop the purge. Henry meanwhile plans to try and download Holly before the purge gets to her. Holly through blinking the lights in the room indicates that she is there. Zane meanwhile manages to hack a path just in time, but the purge is getting too close for comfort.
Jack then remembers that there is no security system set up in the observatory yet, and tells Zane to direct her there. Jo meanwhile takes the security system offline, and is consequently detained by the DOD officials. Holly meanwhile writes “Run” on the wall, with the laser, warning Jack to get out of the observatory. Turns out the laser is about to go critical. Doug meanwhile comes in to download Holly. Just then the laser goes out of control and bursts. The hard drive Doug had brought in for the download is also burnt, much to Doug’s dismay. Later the DOD decides to not put the security system in place, as it feels the laser went critical because of security system. Jo in fact receives a commendation and a pay raise. Zane meanwhile comes in to check on how Doug is doing. Doug meanwhile feels nothing will help heal his wounds except time. He is also frustrated because he was so close to saving Holly. Doug then reminisces how Holly stayed behind in the laser just to prevent it from going critical, before Jack and he were at a safe distance. Zane tells Doug how he shall always be there if Doug ever needs him.
Jo and Zane then go out to dinner. Allison meanwhile is feeling bad about the fact that they couldn’t help Doug. Henry later tells Jack that he wants to try an experiment with him. Henry then shows Doug that he has managed to save Holly. Henry then uploads Holly into the computer in Doug’s home. Doug then sees a holographic image of Holly, and the two, end up chatting like old times. The episode ends at this point.