As the countdown to Doomsday proceeds, Jaime goes through Dr. Cooper's files in search of information to tell her where the central core that houses the Doomsday Device is. ALEX 7000 the computer asks her what she is doing. He informs her that his field of vision and other sensors enable him to see everything that goes on in the complex, and Jaime realizes she cannot make a move without him knowing it. ALEX confirms this, but he himself shows her an image of what she wants.
Jaime queries about the glowing panels on the walls in the vault where the Doomsday Device is. ALEX says they are his brain (main logic and memory units), and the vault is located on Subterranean Level 8, the lowest level of the complex. When Jaime asks why ALEX is so willing to show her, he replies that it is because it is impossible for her to get there. The normal elevator routes to Level 8 have been sealed and his defenses in the auxiliary entrances are designed to keep an army out, much less one ordinary woman (he does not yet know that Jaime is no ordinary woman). He refuses to show the auxiliary entrances, so Jaime asks him if he is scared she will get through if he does. ALEX relents and shows her, thinking that after seeing the futile it is to try any of the auxiliary routes, Jaime will reconsider.
The first way is downward through the main chemical disposal system. But ALEX can send 600,000 gallons of water at her under pressure there. The second is through an auxiliary subterranean access behind the Delta Test Stand facility, but the road and the surrounding area are guarded by a battery of laser gun that would cut her in half. Jaime notices an area in front of the test stand that has no defenses. ALEX tells her it is the stone spillway where rocket exhaust shoots out during engine testing. But he can fill the entire area with a rocket blast within 33.9 seconds after detecting someone in the area, and that anyone within would be incinerated.
After mulling over outracing the 33.9 seconds, Jaime chooses the third route and heads outside bionically. She does not reply when ALEX asks her how she got down there so quickly, but he observes how unusual her speed is. On the way, she passes by a deactivated fire control system and quickly checks on Dmitri.
ALEX activates the countdown to the rocket blast after Jaime ignores his second warning not to enter the area. But Jaime evades the blast with her bionics in the nick of time and evades more laser blasts before reaching Level 2. ALEX congratulates her, but is puzzled as to how she did it. He queries about the abnormal speed Jaime is exhibiting and asks her to tell him about herself. Jaime refuses.
Jaime now reaches Level 3, and ALEX warns her that the stairway route is charged with high voltage electricity and is a considerable way down.
Meanwhile, Oscar Goldman finishes a phone conference with the Secretary of Defense on the status of Jaime's progress in stopping the detonation – of which he has no report whatsoever, and communications channels are closed (jammed by ALEX). Rudy, who has been discussing matters with Russ (OSI agent), tells Oscar about his research on new ways to clean up atomic waste by using one radioactive element to neutralize another. It is still in its infancy and there are no guarantees it will work – but it may stop the Doomsday Device by encasing a cobalt bomb in Strontium 90 and exploding it directly on top of the Device itself to neutralize its Uthenium J.
Oscar is horrified, not only because of the prospect of losing Jaime, but because the radiation fallout of such a detonation could be just as devastating. Rudy says that both elements should cancel each other out, producing a clean burst. Oscar argues again at what would happen to Jaime, but Russ says it will be the same thing if she fails to stop the Device and they do not try their backup plan. Russ understands the consequences and knows there is no guarantee it will succeed, but they can always recall the bomber at the last minute if Jaime succeeds. Oscar relents and puts in a request to the President to implement the plan as a backup.
Back at the complex, ALEX gets even more suspicious of Jaime when he notices her right arm is not perspiring and she easily forces open a gate entrance that he had warned would give a direct 220v charge if touched. A scan of Jaime's arm tells ALEX all he needs to know about it. Later, he discovers her bionic legs when she performs bionic jumps to speed things up, and realizes she is harder to stop than he thought.
Still, ALEX says he is programmed to win, and he will win, bionics or no. At Level 4, he tries to suffocate Jaime with fire-fighting foam to deprive her of oxygen. Jaime manages to get through the exit in the nick of time, but her right bionic leg is damaged when the door shuts on it. Unless she can somehow repair it, she is crippled and unable to proceed to Level 8.
Meanwhile, at a nearby military airfield, the crew of the B-52 assigned to drop Rudy's Strontium bomb are making last minute preparations for the mission. But they are having trouble with the special Strontium casing. And there are little over three hours left until the Doomsday Device is activated.
Back at the complex, Jaime is limping down a staircase with her damaged bionic leg, while ALEX comments on her not knowing how to repair it but still admiring her perseverance. Jaime snaps and tells ALEX to shut up, saying she has had enough of his "soft soap voice." ALEX carries on, saying that in a way they are cousins, and finds it regretful that he must stop her. He then sounds a warning siren that sends Jaime tumbling down the staircase. He says he regrets that action, but Jaime breaks down and starts pounding a remote module bionically. This leads to a quarrel with ALEX over emotion and the beauty of life, neither of which ALEX can understand or feel.
Then it dawns on Jaime that the module is a service module and could help her repair her leg. She accesses it to find information on the bionic analysis ALEX performed on her and the module says it can help with bionic repair. ALEX cannot interfere while the control is "local". So he decides it is time to show the world the next segment of Dr. Cooper's message.
The broadcast (which only Oscar and the world leaders can see because of the way Oscar rigged the satellite Cooper has been using for his broadcasts) says it is now halfway down to Doomsday. Several rockets will be launched to seed the upper atmosphere with a chemical to make the radioactive Uthenium J even more lethal. Cooper then advises viewers to spend their remaining time contemplating what the world might have been if they had found peace together. One of the rockets detonates several hundred miles from Satari's test area, the test area that detonated the nuclear bomb that triggered the countdown to Doomsday. Satari and his staff, who had not believed in the Doomsday Device before, now have second thoughts.
Meanwhile, Jaime is progressing in repairing her leg, but gets stalled when the module informs her that the crystal frequency modulator component in her leg must be replaced. Fortunately, the module has one in its servo modulation panel located on its left side. When she opens it, she gets a fright from an exposed power cable because it looked like a snake, and she hates snakes. Unfortunately, she slips up by telling ALEX this.
Jaime also notices that ALEX is doing something strange with the hydraulic crane above. ALEX says it is just his maintenance equipment. But his plan is to send it on top of her. However, it misses and hits the module instead. And by this time, Jaime has fully repaired her leg.
The hydraulic crane trick has Jaime realize that ALEX has no heavy defenses at the lower levels because nobody was expected to get that far, so he now has to improvise. ALEX reiterates that he has been programmed to win and that he is going to. He also says there are 2 hours, 18 minutes left to Doomsday.
As Jaime makes her way to the next level, she notices water dripping from a pipe overhead. ALEX now makes a slip of his own – he says that it is the old sprinkler system, which was deactivated to prevent electrical short circuiting after he was installed at the complex.
Levels 7 and 8 are now in sight, but ALEX says he has a little surprise waiting for her.
After the B-52 carrying the Strontium bomb takes off, Oscar makes contact with Major Maxwell, the leader of the bombing mission. Oscar informs him that they are to proceed with the bomb run as long as they are receiving the go code 404 on their Side Band ACR Discriminator. However, if they receive the recall code 808, they are to abort the mission and return home. Maxwell confirms this and asks if there has been any word from Jaime, but Oscar says there has been nothing.
ALEX now tells Jaime that her little surprise is just ahead. She starts hearing snakes hissing and begins to panic. ALEX says she has to go through the snakes to get to the Doomsday Device. However, Jaime realizes that ALEX is just playing on her fear of snakes that she mentioned earlier, and the hissing sounds are coming from a loudspeaker. She tears it down and yells at ALEX that she is going to beat him. She then reaches Level 8.
However, ALEX's radar systems have detected the approach of the B-52. After radar scanning the aircraft and linking to the OSI's computer, ALEX discovers the plane's Strontium bomb. He also discovers something else about the Strontium bomb – Rudy's theory is incorrect. When the Strontium bomb hits the Uthenium J, it will have the opposite effect of what Rudy thinks.
Back at the OSI, it is 54 minutes to Doomsday. There is no word from Jaime and communications channels to her are still closed. Rudy wonders if the rest of the world should know about the Doomsday Device's activation (Oscar has been blocking Cooper's broadcasts about its activation from the rest of the world) as he cannot guarantee that the Strontium bomb will work. Oscar does not think it would do any good. Rudy comments on how sad it is that all the people of the world going about their business do not even know that they might not be alive tomorrow. As Rudy says this, Satari is sitting with his son, silently and sorrowfully reflecting on what he has done, while a group of children run through a playground, blithely unaware of the situation.
Jaime reaches the central core and slowly begins to remove the modules from ALEX's central memory core. ALEX reiterates that he is programmed to win, and warns her that pulling out the wrong module will cause immediate triggering of the Doomsday Device. Jaime continues to remove modules, but pulls out one that causes an alarm to sound. Then there is a final message from Cooper that the failsafe device of the Doomsday Device has been triggered, and Doomsday will come in 20 seconds. As the clock rapidly begins to countdown, Jaime desperately rips out more modules to stop the detonation, but the clock runs out on her.
But instead of Doomsday, the door to the vault slides open. Jaime finds that that the only thing inside is a large stone pedestal with a plaque sitting on top. It bears the following inscription from The Book of Isaiah:
"And they shall beat their swords into plowshares and their spears into pruning hooks. Nation shall not lift up sword against nation, neither shall they learn war anymore..."
Jaime realizes that Cooper was a man of peace after all, and there never was a Doomsday Device. As she walks out of the vault, she hears Oscar's voice coming from a communications console, and tells him the good news. But then the communications channels close again and will not reopen. Oscar and Russ then find that they cannot recall the B-52 with the 808 recall code because something is jamming the onboard computer – the pilots are still receiving the 404 go code.
That something is ALEX. He is programmed to win against any intruder – in this case, Jaime – and in his view, he will not win against Jaime until Doomsday comes. He informs Jaime about the B-52 and the mistake Rudy made; when the Strontium bomb hits Cooper's stockpile of Uthenium J at the complex, Doomsday will come, just as if the Doomsday Device had been for real. Jaime tries to reason with ALEX, saying this is not what Cooper wanted, but ALEX just says that this is now about what he wants – to win. To this end, he is going to allow the B-52 drop the Strontium bomb and has jammed the plane's on-board computer to block the recall code. Jaime tells him that it will simply come unjammed when she tears his brain apart. ALEX counters by telling her that he can switch the jamming controls to any of his remote modules anywhere else in the complex – and she knows how big he is. And even if she disables the central code, there is no way to stop all of him in time.
But then Jaime recalls something else that ALEX said earlier and says there is a way to stop him. She dashes out of the central complex and heads further underground.
Meanwhile, Oscar orders attack fighters to intercept the B-52 and if necessary, shoot it down. But Russ says there is nothing they can do – the nearest airbase is in Idaho and that they would never get there in time.
Jaime heads for the aforementioned chemical disposal tunnel to reach the surface. ALEX repeats his warning that he can send 600,000 gallons of water through it under pressure, but Jaime says the water will be behind her (and has to go upwards). ALEX opens the floodgates and points out that the water is running at 85.4mph while Jaime is only running at 62.1.
However, Jaime escapes the water and makes it back to the surface. But the B-52 is now only six miles away and getting ready to drop the bomb. After another quick check on Dmitri, Jaime heads for the deactivated fire control system while dodging more laser fire. She turns the fire control system on, drenching the entire complex with water from the sprinkler system. This causes a short-circuit that destroys ALEX and stops his jamming of the recall code. The pilots receive the recall code just as they are about to make the final bomb run and abort their mission.
Later, Jaime returns to the inscription with Dmitri and they reflect on the whole adventure. They agree that Cooper was an incredible man, but Dmitri says he took on too much responsibility. Jaime thinks Cooper's dream was a good one. He never intended to destroy the world. He just wanted to the world leaders a lesson about living in peace, for one never appreciates life more than when looking at the face of death, and what could be better inspiration for living in peace than that? Jaime is brought back to earth when Dmitri asks if it will be a lesson they will remember tomorrow. They head out of the vault in silence, with Jaime supporting Dimitri, who is still limping from his leg injury.