How did Franklin manage to find Gabe and Lian's second safehouse beneath their notice? They were following a truck containing Pharcom data. A car escorting the truck containing Pharcom data noticed it is the same car the trailed the truck all the way to their destination. One Cutthroat Harvester agent got out, took a photo of the New Jersey license plate. Afterwards, they tagged the vehicle with a tracking device and eventually tagged their safehouse, telephones, and cell phones as well. When Lian and Gabe returned during Syphon Filter 4, they spoke about seeking a safehouse in somewhere in Cordoba Argentina to reduce the travel cost and other expenses and have Lawrence and Teresa stay in the United States in case of more terror attacks. (Starting from the beginning of the game) After moths of finding a home in Argentina they use government business travel, anywhere that the government not affiliated with terrorist permitting them to carry their weapons, ammo, and equipment on board as long as their ID remains valid. Thanks to the persuasion of Carla Loomis at both the Geneva convention the United Nations.
Agent Maksim Finds Franklin's Underwater Facility
After the Black Baton broke in and bugged his telephone, he eventually gets a phone call from Franklin. Convincing Gabe to stop pursuing him, he will have his close partners kidnapped, drugged, and neglected. Gabe was questioned how did he know Franklin decimated all of South America. Pharmacist confessed to the C.I.A. that Franklin is the main investor for Pharcom and funded South American governments and cartels into doing whatever he requests.
Immediate Ambush
Two dilemmas during the phone call. Gabe must surrender and escorted back to Washington D.C., then he will be pardoned by South American governments, leaving Franklin continuing to flood South America with crimes but will never return to North America or Europe anywhere close to the future. If Gabe refuses, he gets executed in Colombian prison and his associates will be completely crushed. Gabe couldn't risk it and calls for backup.
Lian Spots 2 Spy Boats
After spending years laying low beneath Mara Aramov's radar, Maxim spent 2 days scoping out Franklin's hidden underwater island facility. Because no one has the key to go into the main entrance, he found the cave exit. Lucky for him, no access key is required to breach the exit.
Coche Island Fortress
Ambushed by Cutthroat Harvesters, finds dead ends and explosive traps, no radio signal, Lian runs in a shouts for Gabe and Maksim. They all left the facility together. The ATF squad stayed outside and kept on the lookout.
Lian reconned the ocean boarding Venezuela and eventually spotted 2 spy boats driving towards Coche island. Everyone quickly boards the boat and trails the spy boats. Dusty is the only person with explosives and wanted to plant one at the front in case there is no other way for them to get in. It was probably too risky.
The 3 agents finally caught up to where the boats landed. Unfortunately they cannot get in the fortress due to it being heavily guarded. With very careful planning, the 3 used stealth and took out the guards outside on the walk way and their spot lights. They broke in through the back entrance where there were only 2 more guards. They took them out and disabled their security network.