2007: East Asia Crisis Edit
During the 2007 East Asia Crisis, a blackout hits Japan and the US Eastern Seaboard, plunging New York City into darkness. Believing the blackouts to have been engineered, Third Echelon Director Irving Lambert sends Sam Fisher to Abrahim Zherkezhi's Penthouse to investigate the cause of the blackouts and to find out who Dvorak really is. Sam infiltrates the Penthouse to find it guarded by the same mercenaries that were protecting Hugo Lacerda. He questions one of them to find out that they work for Douglas Shetland's PMC Displace International. Fisher soon finds out that Dvorak is in the building next door and that the guards in Displace took orders from the V.I.P Protection Director Milan Nedich. There, an elder man reveals that Dvorak is an infinite state machine, so Sam retrieves the output stack as a means to track down the source responsible for the blackouts.
Sam then goes to Displace Offices to find out if Displace and Zherkezhi are working together. Sam infiltrates Displace and heads to the server room only to find out that Nedich erased the info they needed, and the power comes back on as Sam retreats from the server room. He then makes his way to Nedich's office and on the way he overhears a conversation to find out Milan Nedich is really Milos Nowak, a Bosnian war criminal. Sam then taps Nedich's computer to find out he moved Zherkezhi to Hokkaido, Japan and then Sam extracts from the rooftops.
After the truce in which North Korea agreed to withdrawal from Seoul, a rogue North Korean Colonel Kim refused to lay down his arms and took control of Grand Central station with a sizable force and initiated a standoff with authorities. A rookie splinter cell team was subsequently sent in to defuse the crisis, but failed in preventing Kim and most of his men from leaving.
After intercepting a communication between Kim and a corrupt North Korean CGIB minister who was under Third Echelon's radar, it was revealed that Kim had infiltrated the United Nations headquarters. The splinter cell team was subsequently sent in and was able to kill Kim and defuse a bomb that was set to go off in the ventilation system.
2008: JBA Operation Edit
Version 1: JBA Headquarters/Coast Guard Boat Edit
After escaping Ellsworth together, Jamie leads Sam into the JBA Headquaters in New York City, where he meets Carson Moss. Moss takes Sam to the training course and there he completes the course, bugs their antenna and puts a trojan on their server and returns to the course. Moss then takes Sam down to the interrogation room where he meets Emile Dufraisne (Version 1). Emile then orders Sam to kill a hostage named Cole Yeager. Sam can then choose to shoot Yeager or not.
Later outside the HQ Lambert and Sam have a talk before Sam returns to the HQ. When he does, he finds Enrica and she takes him to the mine assembly room where he makes some mines. After Sam does so, and heads to Emile's office where he steals the notes from his safe. He then makes his way to another building where Sam finds Enrica and they have a short talk.
After the operation in Cozumel, Sam and Lambert have a short talk at the gates to the JBA HQ and then Emile takes Sam down to a computer where Emile has Sam decrypt an email message. Sam does so and takes both the disarm code and visual proof of the bomb before heading back. When he gets back, Emile takes Sam to main room to watch the ship blow. Sam can then not destroy the ship, frame Enrica for it or destroy the ship.
After Kinshasa, Sam, Emile and Moss have a short talk on the bomb and then Emile takes Sam and Jamie to the interrogation room where Lambert was caught in the HQ. Sam can kill either Jamie or Lambert (though the canon choice is to kill Lambert.) Sam then questions Dayton to find out that Emile has retreated to the lower floors where the bomb is. Sam follows him to only find out he intends to detonate the bomb in a few minutes. In the nick of time, Sam kills Emile and defuses the bomb. Shortly, SWAT shows up but Sam slips out to the sea.
Coast Guard Boat: Sam slips onto a boat where Moss intends to detonate a Red Mercury bomb in the middle of New York Harbor. As the Coast Guard closes in, Sam infiltrates the boat disguised as a SWAT officer and attacks Moss from behind, killing him and disarming the bomb. The Coast Guard then arrives and opens fire on the ship. Fisher jumps clear of the vessel just as it explodes.
Version 2: Grand Central Station/Skyscraper Edit
Unlike Version 1, the JBA headquarters is located in New Orleans, Lousiana. Only two missions take place in New York. The first occurs after the first mission at the HQ, in which Sam must help the JBA rob a money train and use the money to find out who stole the Red Mercury from Iceland and to buy some. Sam and Enrica infiltrate the station and eventually Sam finds the station chief. Emile orders the chief's death, but Lambert commands no casualties. The choice is up to the player, and affects trust signifcantly for the corresponding side. Afterwards, Sam boards the train and makes his way to the front car after disabling the communications network. The train crashes to a halt and the JBA takes the money.
The second mission in New York is the final mission. The JBA has placed three Red Mercury bombs on two high buildings in Manhattan. The first building holds the first bomb along with Jamie, B.J. Sykes, and Sykes' men. The second building is where the other two bombs and the rest of the JBA are. Prior to confronting anyone, Sam meets Enrica and the two plan on running away together after the bombs are disabled. On the 68th floor, Sam makes his way through Moss and his men, all equipped with night vision, and disarms the second bomb. On the roof, he neutralizes Emile's men. Emile himself engages in a fight with Sam, but Sam is victorious in the end and disarms the final bomb. Shortly after, Enrica looks for Sam but is shot by a Splinter Cell sent by Lawrence Williams. After Enrica dies, Sam kills the Splinter Cell out of anger and removes his cochlear implant, ending his career at Third Echelon.