This article contains endgame spoilers, read at your own risk.
This is the primary objective of this game, to kill Lucas Santino. His base of operations is in Sector 1, and securing it ends the game. This is no easy task. Good luck, commander.
Sector 1
In this sector, there are two islands: one surrounded by a body of water, connected with bridges, and covered with many bushes. The second has a single bridge and contains a large compound with the northeast coast walled up. The lake in the middle has Metavira Eels water snakes in it. The bushes provides plenty of cover for the enemies, and great for grenae throwers to ambush your mercs with Stun and Mustard Grenades. Santino's compound is in the northerneast part of the sector.
The enemies are equipped with various weapons (from .38 revolvers to M16s) and maybe various armors. The .38s and Colt .45s may not be life threatening for a merc that is wearing a Treated Spectra Shield, but they can drain energy and potentially knock out the merc.
Most of them carry Mustard and Stun Grenades, and these enemies have very good throwing range, so distancing yourself may not always work, especially when crossing the bridges. Equipping a Gas Mask is recommended, to reduce the amount of health and energy taken. Equip your team with such grenades to return the favour.
The enemies will re-spawn up until you exhaust Santino's staff pool, which takes a siege of several days of intense firefight, unless you manage to enter the northwestern building. Exiting said area will resume the re-spawning.
Confronting Santino
"You've run out of luck.... I'm going to blow this place and the Fallow sapling with it! We'll meet in hell!" - Lucas Santino's final words
Once you reach Santino's room which is the northwestern room, he interrupts whatever game action is in progress and gives a speech. At the end of the speech, he sets off a self-destruct mechanism, which causes chains of explosions at different locations in the room every turn, killing himself in the immediate 1st explosion and hoping that it will kill your mercs in the process as well. After the mercs are done stating that the building will explode, you must get every merc out of the building or they will die in the explosion. You will be congratulated and the credits will roll afterwards.
(Spoiler) At the desk in the corner of the room, there is the Fallow sapling Santino mentions. (This was mentioned in a piece of paper in sector 33). You must grab it quickly before the explosions destroy it and manage to get the corresponding merc out in one piece. Probably the best way out is the western wall as the 2nd(?) explosion blows a hole in it. Securing it intact, securing its remains, or failing to do so, will affect the final cut scene.(Spoiler)
Whatever the outcome of the assault, recovery and evacuation, game ends 3 to 5 turns after Santino sets the bombing sequence.