A fully manned US Naval supply ship is boarded by Somali... pirates, from these?The Assault on the U.S.S. Mt. St. Helens was a major conflict of Syphon Filter: Logan’s Shadow in which multiple factions of the United States of America were deployed to secure the contents of cargo hold 5 on the said ship, a naval ammunition supply vessel which was boarded and hijacked by Somali Pirates and al-Jamil terrorists. While the antagonists possessed inferior equipment and were considerably inept, and contrary to the fact that the Americans were much better trained to handle such a threat, the event ended with Ghassan al-Bitar fleeing with the classified contents, while Robert Cordell caused the ship itself to be scuttled in an attempt to hinder or terminate the terror agents. Gabe Logan was eventually forced to dive into the ocean to save himself.
The confrontation began when Robert Cordell deliberately ordered the ship to be left alone, without an escort, in the Indian Ocean, and hired Bitar to acquire the Chinese scientific Einstein, Shen Rei, before competing nations could do the same. Bitar used waves of thugs to overrun the St Helens, slaughtering the entire crew, and tried to gain access to cargo hold 5, which held highly restricted material transported by Cordell. Subsequently, the NIOC director ordered Special Forces to the scene, but the soldiers failed due to the pencil-neck's withholding of vital information. Gabe Logan was then persuaded to head on-site to settle an old score with Bitar. In a bittersweet twist of irony, Cordell later ordered that Fifth Fleet fire on the vessel to stop Bitar from escaping, but failed.
The initial attack
Did you get the codes?
He wouldn't talk.
Throw him overboard and find the captain. This time I will do the questioning.
-Ghassan al-Bitar and a Somali thug confer
When the pirates first attacked the St. Helens, it was a battle of attrition: their foot soldiers died in the masses, but they kept sending men to overtake the boat. They ultimately conquered the security forces and took controls of the ship's weapons systems.
Conference with Cordell
We don't have time to go over the details, Logan. We need you on site now. Transport's standing by.
Let me just get this right. A US Naval supply ship is attacked by Somali... Pirates, from these?
We don't know how. That's why I'm sending you.
Because the Somali's want the contents of hold five.
I never said they were after hold five. I only said, I need you to secure it.
-Cordell and Gabe discuss the incident
Called up on the phone, Gabe and Teresa watch Robert Cordell brief them on the circumstances: a group of al-Jamil pirates have seized the USS Mt St Helens and Logan is requested to be onsite to secure the contents of hold 5. When Gabe questions Cordell on what exactly is being transported, the NIOC director tells him it is classified, need-to-know, but under no circumstances can the Somalis acquire the material. Despite Teresa's reservations that this assignment is beyond IPCA jurisdiction, Gabe agrees to go, although he tells Cordell he will use his own personnel, and intends not to stop Bitar at the behest of the NIOC, but rather because of an old score he has not yet settled with the terrorist. He tells Alima to prepare her gear, and requests that Teresa recall Lian from her holiday. 
Approaching the ship
Chief, I'm picking up a distress signal.
From the ship?
No, Special Ops...code blue. Sounds like they're in trouble.
-Alima reports to Gabe
Upon arriving onsite, Gabe realises his pilot has intercepted a distress signal, broadcasted for several hours, and suspects that things may not be what they seem. He destroys the St. Helens’ CIWS missile launchers before landing, and fights his way to the distress call’s source. Along the way, he encounters the body of a US Special Forces, and realises Cordell relied not only on the IPCA, but also called on US military personnel; specifically, Special Forces.
Damn it, we're too late. He's dead.
Why didn't Cordell tell us Special Forces were onboard? Did he think that would've scared us off?
Then he underestimated us...again.
-Teresa and Gabe converse
After terminating a considerable amount of pirates on deck, Gabe arrives in a corridor with a wounded soldier and contacts Teresa, telling her to get Cordell online. From the dying troop’s last words, he determines the attack was complex enough for Bitar to be the brains behind it.
Second downing of Alima's chopper
Continuing his search, Logan takes down squads of enemies and establishes an uplink to the St. Helens communication system. His pilot is shot down and he rushes to rescue her, but she dies. Gabe endeavours to destroy the pirate boats.
Destruction of the Somali vessels
I'm at the bulkhead. They've ripped a hole in the side of the ship.
-Gabe reports the St. Helens damage to Teresa He finds a stash of C4 explosives and uses it to detonate a number of vessels, opening a passageway into the St. Helens lower levels.
Fifth Fleet is firing missiles on the St. Helens. They're trying to scuttle their own ship.
-Teresa tells Gabe about Fifth Fleet Entering the cargo compartment, he kills waves of pirates and finds that the cargo has been stolen. He attempts to shoot down Bitar, but Fahid Tamer intercepts him; the fight ends when he kills the enemy. Finding the St. Helens is being fired upon by the Fifth Fleet, he dives into the ocean just as a destroyer’s cruise missile impacts on the doomed boat, sinking it.
With the vessel scuttled, a new antagonist had set their sights on it - the Russian Spetsnaz Alpha squad. They dispatched a team of elite naval commandos to search the area and find anything interesting, with Kudrenko's right-hand man, Surgeyev, supervising the operations. Sea mines were deployed to deter parties attempting to close in, while a Soviet Stalker Submarine was also sent out to provide reinforcements in case any intruders attempted to encroach on the wreckage.
Behind the scenes
- It is revealed in 'Dead Currents'`that the St. Helens was not a true US Naval ship.
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