The Second Destruction of the SS Lorelei was a major confrontation of Syphon Filter: The Omega Strain in which Gabe Logan resolved to permanently scuttle the remnants of the Syphon Filter virus following a botched attempt to sink the Lorelei with MI6. He was finally successful, using a nuclear weapon, which Stone had earlier appropriated from CIA headquarters in Langley, Virginia, to achieve the desired effect.
Despite the mission's success, the IPCA soon became the object of the President's scrutiny after Alex Birchim informed Warren H. Pierce of Logan's actions. William Crusher was killed in action, and Nikolai Jandran, who was supposed to be captured alive, eventually died as well.
Contact with Niculescu
Mara Aramov contacts Mihai Niculescu, telling him that Ivankov is blackmailing the Politbureau and that he refuses to bring her to his base. Niculescu reminds her they can't wait, and tells her to take care of Murukawa while he will deal with the others. The call ends with him telling her to find Ivankov's base.
Meanwhile, Gabe's team moves in to the salvage rig operation in the North Atlantic. Mujari tells the recruit he will go to the deck control tower and patch in from there while Crusher holds position on the flight deck.
Search for the salvage personnel uniform
With Mujari installed on the tower, the recruit heads into the rig, attempting to disguise himself as a salvage worker. The agent first acquires the access codes required to gain entrance to the highly restricted Level 13 while incapacitating collateral targets and using lethal force on armed security. Upon gaining the codes, the recruit heads to the upper levels and blends in with the workers using the uniform. Before continuing, he acquires a sample of the original virus, synthesised from the Lorelei's cargo.
Rescue of the workers
After acquiring the uniform, the recruit heads to the lower levels, and an accident is soon triggered. Mujari is trapped on level 2, while a group of workers is drowning. On the topside deck, Crusher attempts to fend off incoming Meta Global copters.
The agent hurries to level 3 to activate the emergency pump system, and then to level 5 to carry the unconscious workers to safety, allowing them to use the lifeboats. With that, they head to level 2 to unlock a door that traps Mujari. Crusher is eventually killed, sacrificing himself so the others can continue their mission.
Infiltrating Level 13
Using the elevator, Mujari and the recruit head to level 12, and hack into a security system that opens a blast door leading to Level 13. From there, the duo shut down a minisub before it can be deployed, while the recruit hurries to catch Dr. Jandran, in order to administer a vaccine to him. The serum, however, has an adverse reaction; the agent heads to the lower levels to deploy the nuclear device.
Planting the nukes
With the explosives placed, the agent takes down a security detail sent to kill intruders and returns to Level 13. Another wave of guards is sent down, but neutralised as well. With their mission complete, the duo orders a mass evacuation using the PA system and then escapes using the minisub.
With Syphon Filter finally neutralised, Gabe would come under fire from Alex Birchim for detonating a nuclear device, and was ordered by Warren Pierce to report the reasons for his actions. Meanwhile, Lian Xing leads an assault on Murukawa Industries in an attempt to capture its leader for interrogation.