The episode begins with Henry panicking about the main reactor not responding to the restart code. He is then informed that the power in the reactor is falling. Jack is then informed that Eureka is under attack by someone unknown. He is also informed that all the communications of the facility are down, and their radar is tracking an incoming missile. Their missile shield is down so the only option left for them is to shoot the missile down. After impact certain levels of the facility catch fire. Jack is given the responsibility of taking Douglas to a secure location. Allison in the meanwhile is attending to the casualties. Meanwhile, just as Zane opens a blocked door and helps the people to escape with Jo overseeing the whole thing, it is informed that the facility has been contaminated with Ammonium Chlorate gas.
Meanwhile, Douglas and Jack discover that as a result of the evacuation protocols kicking in prematurely, Douglas’s office has taken off for a bunker without him in it. They then decide to take an emergency staircase which is 72 flights down. Jack is then informed that Douglas has broken a leg and has to be carried down the flight of stairs. Jack refuses to do that and walks out, just then it is shown that the whole thing was a disaster simulation. Later, Henry tells Jack that Grace is taking her own time to recover from all that has happened. Henry then introduces Jack to Dr. Michael Clark, who their severe accident phenomenologist. Clark basically blows stuff up to see how well prepared they are. He informs them that the simulation has 29 people dead, which isn’t bad and hence the score is a B+. Jack is shocked as to how 29 people dead can be good.
Clark in turns explains that in disasters people die. Jack is also informed that, their future funding from the DOD will depend on the simulation results. Jo in the meanwhile is shown giving Jack the cold shoulder, much to his surprise. Later is it seen that all is not fine between Zane and Jo, with Zane too busy to find time to even have dinner with Jo. Meanwhile, Jack asks Allison if Jo is under stress, and she gives him measured answers. Then, Allison also gives the excuse of work and opts out of spending some time together with Jack. Meanwhile, Zane meets Douglas, who asks him if he has kept under wraps what they are doing. Zane promises him that no one would find out. The two are basically still trying to find out if, there is still any energy signatures of Holly left in the Matrix program. Meanwhile, Clark tells Jack that his performance was bit off in the simulation, Jack in turn isn’t too happy with people actually being injured due to the simulation.
Clark tells Jack to take up with Henry any issues he might have with the simulation. Jack doesn’t want to do so as Henry is at the moment busy fighting battles in his personal life. Clark then tells Jack that, blaming ADA the artificial intelligence for doing her job is unfair. Clark then punches in the codes to open hi lab door, and just as he does, both he and Jack get flung a distance by some pressure release from the inside. Later, it is discovered that a liquid nitrogen valve had ruptured inside the lab, during the simulation, which in turn case the pressure build up. Clark in the meanwhile is hauled away in a neck brace, with a concussion and a collar bone fracture. It is also discovered that ADA the disaster simulator has taken a beating and hence all the disaster drill data and most of their evaluations is lost. Jack feels its sabotage, and Jo decides to look into it. Meanwhile, Douglas is readying to go back into the program with Zane assuring him that, he has got his back on the outside.
Douglas is desperate to see Holly, even if it means seeing just a flicker of her, due to most of the program being scrapped. Douglas then enters the program and begins his search for Holly, in a program which is bereft of any other character. He then finds Holly who is overjoyed to see him. She tells Douglas what had happened to her. The two then kiss, just then Zane brings him back, as he is worried on seeing Douglas’s heart rate skyrocketing. Zane is then surprised to hear the experience Douglas had inside, as he was only expecting a partial render of Holly within the program. Douglas meanwhile feels Holly is alive. Jo meanwhile is doing her best to avoid Jack, but Jack is persistent. She informs Jack that the liquid nitrogen valves were opened deliberately, just as he had suspected. Jack then confronts Jo about her behavior and she tells him that it was because of last time, when the body swapping incident had happened and she had asked him about them kissing, and how he felt about it, and how he had reacted indifferently.
Jack tells her he remembers nothing and apologizes to her. Just then the alarms go off, and they are informed that there is something wrong with the reactor turbine. Jack meanwhile feels that the whole disaster scenario is being replayed, and this time for real. Later Henry manages to get things under control. Meanwhile, Douglas describes to Zane what he saw. The two then, are unable to decide if the Holly inside the program is the real Holly or just a detailed computer simulation. Douglas then goes into the program once again. Meanwhile, Jo comes in and Zane rushes her out of there so nothing is revealed to her. Holly and Douglas meanwhile sit chatting in the program. She is unable to figure why Douglas can come and go out of the program but she can’t. Then just when Douglas is about to tell her the truth, he is hauled out of the program by Zane and told that Henry needs them.
Meanwhile, Jack is outside proceeding to check a cell phone tower that is causing interference. Andy too is on his way to help him. Just then near the tower, Jack sees his vehicle sinking into the ground; he then finds the same happening to him. It is also show that the same thing has happened to the tower, and hence it’s no more a tower. It turns out some underground pipes have collapsed, and the substance that was released has resulted in the soil becoming like quicksand. Andy proceeds to help Jack. Meanwhile, Jo and her security team are near the aggression lab which has breached. It has snakes, tigers, bears and other animals, and hence they proceed with caution. Just then Jo realizes there is a bio-hazard, with her seeing Ammonium Chlorate gas emanating from the ducts. Meanwhile, Jack tells Henry that all that is happening is a replay of the disaster drill, only this time it’s real. He then rushes to rescue Jo. Jack then rescues Jo.
Back in the medical facility, Allison is visibly disturbed to see Jack nursing Jo and showering all his attention on her. Jack later figures out that it’s probably ADA that is doing all of this. ADA probably is looking at the whole thing as an escalation of the disaster drill. The team figures out that ADA must have given the directives before she, possibly self destructed. Meanwhile, as a next part of the drill, the shields go down, and a missile makes its way to the facility, just like in the simulation. Henry in the end decides that evacuation is the best bet, as they have no other options left. Zane meanwhile reveals that he has covertly built an electronic device which might just be able to take down the missile.
Later, Henry gives Douglas directions on the phone which he gives to Jack, so Zane’s device can be placed in an exact location, where it would intercept the oncoming missiles. The device then comes online and manages to neutralize the missiles, much to everyone’s relief. Later, Allison and Jo sort out their misunderstandings. Douglas meanwhile tells Jo that Zane has been helping him out. Later Douglas enters the matrix program to meet Holly. Inside Douglas tells Holly the truth that, she didn’t make it. The two then decide to keep seeing each other in the program. The episode ends at this point.