Valkyrie opens with a Colonel Stauffenberg in Tunisa, North Africa (in 1943), penning in a journal his thoughts about World War II, and how he feels Hitler is destroying Germany. Stauffenberg states he took an oath to swear allegiance to Hitler, but feels he owes more to Germany. He argues with a general about holding a key city in a futile effort against the British Army and American General Patton. The general agrees to have the 10th Panzer moved to a different location where they can be evacuated back to mainland Europe. Shortly thereafter, the camp is attacked by British aircraft and Stauffenberg is badly injured, losing one of his eyes, his right hand, and two fingers from his left hand.
The next scene shows Hitler visiting a base camp in Germany, and a nervous General Trescow onlooking. As Hitler prepares to depart, Trescow and an associate hide a bomb in a wine case and give to a man on Hitler's plane, but it fails to detonate in flight, and Trescow must return to headquarters to retrieve it. Once he arrives, he meets up with who is revealed as a fellow conspirator, a General Olbricht. Trescow safely retrieves the wine case and he and Olbrict discuss a member of their secret committee who was recently arrested. Trescow recommends Olbricht contact Colonel Stauffenberg as a replacement, which Olbricht does, and brings Stauffenberg to one of the clandestine meetings.
In the meeting, Stauffenberg meets three of the most important figures in the resistance: Dr. Goerdeler, who will become Chancellor of Germany should the plot succeed; General Beck, who will lead the Armed Forces, and a man named Witzleben. After tempers flare, Stauffenberg agrees to help. At a later meeting, Stauffenberg suggests they utilize Operation Valkyrie, which is a plan that uses the Reserve Army to keep order amongst the Germany country should anything disrupt communications from Hitler, or should Hitler be killed. Stauffenberg rewrites the order to exclude the SS from taking control, which would leave the head of the Reserve Army, General Fromm, in charge of Germany. Reaching out to General Fromm, Stauffenberg and Olbricht are surprised at his rejection, but Fromm keeps quiet, choosing to neither support the dissenters nor reports them to the authorities.
Meanwhile, General Trescow is sent to the front lines. Stauffenberg is promoted to head of the plan, and he, along with his assistant Lieutenant Haeften, take the order to the Berghof to be signed off by Hitler himself. Hitler, with his inner circle present, praises Stauffenberg's loss of appendages as the attitude necessary for his military, and states Stauffenberg is the ideal German. He then signs off on the bill, saying he's sure the changes are adequate.
Back at command, a Colonel Quirnheim shows the dissenters how to use pencil detonators, and Stauffenberg persuades a General Fellgiebel, who controls communications at the Wolf's Lair, to help. Stauffenberg has been promoted to General Fromm's chief-of-staff, and thus has access to Hitler's military debriefings, so the plan goes as follows: Stauffenberg and Haeften will travel to Hitler's bunker, the Wolf's Lair, to attend a military meeting. Stauffenberg will ignite one of the pencil detonators and then have Fellgiebel call and pretend to be a general, pulling Stauffenberg out of the meeting while Haeften waits with a car. In theory, Stauffenberg and Haeften will have six minutes to drive before the bomb detonates, giving them time to return to the airfield and fly off before they can be suspected. The only condition the heads of the dissenters give, however, is that head of the SS Himmler, along with Hitler, must be present for Stauffenberg to arm the bomb.
Stauffenberg travels to the Wolf's Lair and has all preparations ready, but notices Himmler is not present at the meeting and calls the committee to ask if he may proceed anyways. He is refused by the committee, unbeknownst to Olbricht, who mobilizes the Reserve Army anyways. As Stauffenberg safely extracts himself and the bomb from the bunker, the Reserve Army believes they were just running a training drill, and Olbricht and Stauffenberg are ordered to report to General Fromm, who is outraged they would mobilize the army without his permission. He tells them that if this happens again he will arrest them both.
Dr. Goerdeler has a warrant issued for his arrest and General Beck implores him to leave the country. Goerdeler, Stauffenberg's chief opponent on the committee, hastily leaves and is replaced by Colonel Quirnheim. Colonel Stauffenberg visits his home and tells his wife his plan, and that she and his children must leave, because of their suffering if he should fail. They do so, and Stauffenberg makes his next attempt on Hitler's life as he attends another military debriefing on July 20, 1944. Much to his surprise, the meeting has been moved from Hitler's bunker to an open window summer hut. The blast would be most effective in the pressurized bunker, where the thick walls would deflect the pressure back to the bomb's origin, wiping out everyone in the bunker. Stauffenberg plans to proceed anyways but then notices Himmler is once again not present. He calls the committee to ask permission to continue and they say 'no', but Stauffenberg and Quirnheim privately agree to continue anyways, and Stauffenberg enters the summer hut. He and Haeften arm the bomb in a washroom and place it under the war room table, as Haeften gets the car. Fellgiebel gives Stauffenberg his distraction phone call, and Stauffenberg hastily leaves the hut.
In the war room, an enraged Hitler bangs his fist against the table, knocking Stauffenberg's briefcase, with armed bomb inside, over. A correspondent at the table sees Stauffenberg's fallen bag and moves it behind a table leg opposite Hitler. As Stauffenberg walks to his car, the bomb detonates. Fellgiebel phones Quirnheim, but poor reception keeps Quirnheim from fully understanding what all has happened, only hearing that the bomb has indeed detonated. Believing his job to be done, Fellgiebel orders them to shut off all communications. Olbricht impores Quirnheim to phone back and find out if Hitler really is dead, but the broken phone lines keep that from happening. Olbricht refuses to mobilize the Reserve Army until he has received confirmation that Hitler has indeed been killed, and leaves for lunch. Quirnheim issues the mobilization order behind Olbricht's back, and the Reserve Army, led by Major Remer, mobilize in Berlin.
Meanwhile, Stauffenberg, Haeften, and their driver quickly make their way out of the Wolf's Lair, and Stauffenberg cleverly tricks soldiers into opening checkpoints for him. He makes it back to the airfield, and quickly flies a plane back the government district of Berlin.
Much to his shock, the delay caused by Olbricht issuing the order could substantially set the effort back, but they proceed with the plan as scheduled. They march to General Fromm's office and inform him that Hitler is dead, and that he can either join their cause or be arrested. Fromm calls the Wolf's Lair, whose communication has been restored, and hears that Hitler is, in fact, alive. Stauffenberg dismisses this and asks Fromm whose side he's on. Fromm attempts to arrest Stauffenberg and Olbricht, but is himself arrested. Stauffenberg, Olbricht, and Beck, as heads of the Reserve Army under Operation Valkyrie, give orders to arrest all SS officers and seize control of Berlin. Major Remer follows these requests until he reaches the SS headquarters in France. Contradicting orders have been sent, one from the Wolf's Lair ordering the arrest of Stauffenberg, and one from Stauffenberg ordering the arrest of Minister Joseph Goebbels. Goebbels, shown slipping a cyanide pill in his mouth as he watches the Reserve Army approach, picks up a phone and asks to be connected. Remer walks in and states the man is under arrest, but the man gives Remer the phone. Hitler is on the other line, and he commands Werner to release all SS and capture those in charge alive. Remer cancels the occupation of Berlin and marches to Stauffenberg.
Rumors are swirling that Hitler is alive, which Stauffenberg dismisses as SS propaganda. But gradually, Stauffenberg's associates in headquarters are defecting. The Reserve Army reaches headquarters, and Stauffenberg, Haeften, Quirnheim, Olbricht, and Beck attempt to leave. After a short shoot-out with loyalist SS officers, Stauffenberg is wounded. He and all of the other conspirators are captured, and General Fromm is released from his cell. Wanting to appear innocent, Fromm orders the immediate arrest of the conspirators. In his office, he condemns Stauffenberg, Quirnheim, Olbricht, Haeften, and Beck to death, but allows Beck to kill himself with a pistol.
At midnight, the remaining four are taken outside and executed by firing squad in the building square. Meanwhile, General Trescow, hearing of the failure, is shown committing suicide on the front lines with a grenade. Goerdeler is shown executed by hanging, and eventually Stauffenberg is brought before the firing squad. Quirnheim and Olbricht have already been executed, and only Stauffenberg and Haeften remain. Stauffenberg is prepared to face his death when Haeften steps in front of him, taking the firing squad's first shots, and falling dead. The firing squad reloads, and aims at Stauffenberg, who screams "Long live sacred Germany!," before falling dead.
Witzleben is shown publicly denouncing Hitler at his trial, and the film reveals he too was executed on September 4, later that same year. Then the film states that General Fromm's hasty executions could not save himself, and he too, was executed for not reporting the conspirators.
The film concludes with a byline announcing Hitler's suicide in April 1945 nine months later, and reveals that Stauffenberg's wife and children survived.