Ten days prior to the opening of the main game, Third Echelon agent Archer and Voron agent Kestrel are deployed to Nevsky Prospekt in Saint Petersburg, Russia to halt rogue elements of the Russian military from selling advanced warheads on the black market. Intelligence from Andriy Kobin has pointed to drug and human trafficker Valentin Lesovsky as the broker for the sale, and Archer and Kestrel are to terminate Lesovsky and his associate, Boris Sychev, as well as gaining Lesovsky’s contact list.
Having completed their mission, Archer and Kestrel are deployed to the Russian embassy in Baku, Azerbaijan to gather intelligence on an arms deal conducted by former Russian GRU colonel Leonid Bhykov. They observe the deal and see Bhykov betray his associate, Tagizade, ordering his men to kill him. Archer and Kestrel prevent the destruction of the weapons crates, learning that the weapons Bhykov was going to sell were Block II JDAM missile guidance kits. They interrogate Bhykov, learning that he is working with Major General Kerzakov, who is in the Yastreb Complex, an underground fortress situated underneath Moscow’s Red Square.
They infiltrate the complex and learn the location of the EMP warheads. They render the JDAM kits inoperable by using their portable EMP devices, and download data from multiple servers to trace the EMP devices to the Mozdok Proving Grounds. Sneaking aboard a supply truck, they infiltrate the Proving Grounds and secure the EMP devices with the help of Kobin. However, during the middle of extraction, Third Echelon director Tom Reed contacts Archer and orders him to kill Kestrel. Kestrel learns of the order from reading Archer’s OPSAT device, forcing him to act in self-defense. Either Archer or Kestrel can survive, and Kobin then executes the survivor in the next cutscene.
The events of the game take place three years after the events of Splinter Cell: Double Agent. Former Navy SEAL Victor Coste is held in a Black Arrow facility interrogation room as he is interviewed by an unidentified group of men. He then begins to recount the events of Splinter Cell: Conviction in the past tense. This continues throughout the game, with each level narrated in the past tense as the player “experiences” what happened.
After having disappeared, Sam Fisher is located and contacted by former Third Echelon colleague Anna “Grim” Grímsdóttir in a marketplace in Valletta, Malta where he is investigating rumors that the hit-and-run death of his daughter Sarah might not have been accidental. He is warned that a group of hitmen have located him. Sam kills them and interrogates the leader, Dmitri Gramkos, learning that drug runner Andriy Kobin was responsible for Sarah’s death. Sam learns that Kobin is in his mansion, a re-purposed museum. He infiltrates the mansion and, after a firefight with Kobin and his guards, Sam interrogates Kobin, who reveals that there is a conspiracy going on that that is “bigger than” Sam’s situation. Sam is then captured by Third Echelon agents.
He is relocated to Price Airfield in Virginia, where he is to be interrogated by Grim with support from a PMC called Black Arrow. When they are all alone, Grim kills a guard and reveals that she is working with President Patricia Caldwell as a mole inside Third Echelon, and that she needs his help with investigating Director Tom Reed’s relationship with the PMC. Sam initially refuses to help her, but relents after being told that Sarah is alive, and that Grim would prove it to him during the course of the investigation. She facilitates Sam’s escape from the airfield by providing him weapons and access to her car. At this point, Sam calls in Victor Coste, a former squad mate, who rescued him during Operation Desert Storm. Sam meets with Victor at a county fair at the Washington Monument, receives some equipment, and learns that White Box Technologies, an R&D company specializing in EMPs, has hired Black Arrow for corporate security, which is considered out of character as Black Arrow does not normally provide such services.
Sam heads to White Box Technologies and witnesses multiple scientists murdered by Black Arrow operatives. He saves one of the scientists and learns that Lucius Galliard hired Black Arrow to provide security, and a Black Arrow officer known as Robertson has been collecting and disposing of experimental data with EMP countermeasures. On the way to Robertson’s office, Sam gets a phone call, facilitated by Grim, from Sarah, revealing that she is still alive. Sam then reaches Robertson’s office and downloads the data for Grim’s analysts to study. He later triggers an EMP to prevent Black Arrow’s tracing of the download in order to maintain Grim’s cover also frying Robertson in the process.
Sam is later directed to the Lincoln Memorial under orders from both President Caldwell and Grim, in order to infiltrate the area and record a conversation between Reed and Galliard. Sam then interrogates Galliard, who reveals that the operation was funded and organized by an unknown group known as ‘Megiddo’, and that Tom Reed is simply “hired help.” Before he can reveal anymore, Galliard is shot by an unknown gunman. Sam pursues the gunman, only for the gunman to get killed by a car bomb. Sam is immediately drawn into a confrontation with Third Echelon agents until he is extracted by the Secret Service.
Later, Sam infiltrates Third Echelon headquarters to recover equipment from an ally named Fryman and retrieve information from Reed’s office. Instead of finding Reed, Sam re-encounters Kobin and interrogates him again, leaning that Reed was working with Megiddo to smuggle EMP technology into the United States (which was what was happening in the Prologue), and activate the technology as a cover under which to assassinate Caldwell and have Vice President Calvin Samson take over the position, as he was “in Megiddo’s pocket.” As a result of facilitating the assassination, Reed would be promoted to the higher ranks of the government and be considered a hero. Kobin later reveals that he never knew anything about Sarah and only provided a false body to stage her death, urging Sam to ask Grim as she knew the whole story. Sam confronts Grim (via video communication) with the information he has learned, and is urged to listen to an audio recording of former Director Irving Lambert made shortly before his death in New York. Sam learns that Lambert had found out that there was a mole in Third Echelon who planned to use Sarah as leverage against Sam. In order to protect both of them, he staged Sarah’s death as a car accident and secured a similar looking body from Kobin, in order to allow Sam to do his job. Despite this, Lambert concludes that he wasn’t able to locate the mole, and that his efforts may have been in vain. He then escapes the Third Echelon HQ which is promptly demolished by a series of explosions triggered by Reed.
Grim later tells an enraged Sam to stop an EMP attack at the Michigan Avenue Reservoir, stating that Sarah’s apartment is within Michigan Avenue’s radius. Meanwhile, Grim will accompany Reed to the White House in order to halt the assassination attempt. Sam then escapes Third Echelon when Reed activates the self destruct protocol, destroying the building. He then gets to the EMP site at the reservoir, and interrogates a Black Arrow officer outside the compound to discover that a scientist captured by Colonel Jeremy Prentiss is being held captive and forced to oversee the EMP. After witnessing the scientist being beaten by Prentiss, Sam infiltrates the room where the Scientist is being held captive and rescues him, learning that two generators are powering the EMP, and if one EMP generator is destroyed, the other will pulse and trigger the EMP. As Sam reaches the first generator, he asks for Victor Coste’s assistance in taking down both generators, and marks the generator for Coste to destroy. As Sam nears the second generator to mark it for Coste’s helicopter to destroy, Prentiss arrives in his gunship and attempts to kill Sam. He evades Prentiss’s gunship and marks the second generator. Coste arrives and shoots down Prentiss’s gunship, then destroys both generators. Sam is then extracted by Coste and has a brief reunion with Sarah before the two remaining EMP’s are activated, destroying most electronic devices in the city and causing general chaos. After the attack, the helicopter is shot down by a surface-to-air missile. Coste takes Sarah to safety, and Sam journeys through downtown D.C. seeing the chaos and fear the EMP’s have caused, and infiltrates the White House, confronting Black Arrow contractors, renegade Splinter Cell agents and Third Echelon assault troops in the process. Since Reed was able to deactivate the security systems, they were able to kill the Presidential Secret Service detail and take control over the White house. After ‘securing’ the corrupt Vice President, Sam regroups with Grim, who shoots Sam in the shoulder so that he can get close to Reed, appearing to be a hostage.
Upon entering the Oval Office, Reed prepares to execute Sam and the president. Reed reveals that Caldwell was going to shut down Third Echelon and leave America potentially vulnerable without its intelligence services, and tells Sam that the president believed that all the sacrifices Sam and agents like him made weren’t necessary anymore. To prevent this, Reed planned to frame Sam for assassinating the president as supposed proof to the country that Third Echelon was still needed. As Reed gets close to Sam, Sam disarms him and he and Grim kill Reed’s Splinter Cell escorts. Sam interrogates Reed while United States Army soldiers extract Caldwell. It is then revealed that Reed was the mole Lambert was looking for; and depending on the player’s choice, Sam or Grim execute Reed. If Grim executes Reed, she confides in Sam that he is the only person she can trust, but Sam says that he no longer wants to be a part of this and leaves. If Sam executes Reed, he simply leaves the dead body where it belongs.
The story then returns to Coste’s interrogation. He states that Sam’s last conversation with him revolved around the importance of “always having to come back for family,” and how Sam finished that same conversation by saying he loves Vic “like a brother.” Victor concludes his statement by saying “Brother. That’s family right?”, and an explosion rocks the base. Victor then says, “Yeah. I thought so”, implying that Sam is assaulting the base.