The following is a short reference chart to all missions currently active in the game. It's based on game files and it's not meant to be exhaustive (some missions might be still hidden as normal dialogue). In the future this might be expanded to a full walkthrough, but as it stands now it's just a simple check-up list you can confront to make sure you finished all missions. If I missed any mission you know of, please add it in comments and I will update the guide.
TRIGGER: Marion (radio)
Look for survivors at the Helicopter crash
Reward: 10000 virgins
The quest to get to Garcia
Reward: 9001 virgins
Check on Farmer Miguel
Locate Farmer Miguel's Daughter at Lilitu Prison
Reward: Vicky 1 week contract & free shotgun
She's in a cell prison in Lilitu. You get her under contract for a week for free. When you return to Miguel he also gives you a free shotgun. Doesn't mention it, check inventory though after you end dialogue.
Pay Your Respects
TRIGGER: Gabriela (Badilla)
Deliver flowers to the gravesite in Lilitu Prison; when you talk to Gabriela you get the flowers in your inventory automatically (make space) or in the squad inventory.
Reward: Warm Fuzzy Feeling + item from Badilla's citizen representative
Go to the prison cemetery, walk near the graves toward the entrace to the courtyard with the merc that has the flowers in the inventory. You will get a message when you hit the right zone saying you paid your respect. On return the NPC who greets you in Badilla calls you over and gives you a free leg ammo pouch.
TRIGGER: Spice (Badilla)
Talk to the ferryman
Reward: $2000, opens route to Garcia
TRIGGER: Gomez (Badilla)
Buy a piece of map from Gomez, find the other 2 missing parts, locate the secret treasure
Reward: a treasure? that's secret?
TRIGGER: Hugo (Marino)
He's looking for the heads of 3 wanted criminals who are hiding in various locations on the island. Read the posters to get location information. When you deliver quest back to Hugo you need to have heads in the inventory.
Reward: $1200 / head
Diego Gonzales is in D6, Tajo DaSilva is in E10 and Damion Weathers is in sector A11.
TRIGGER: Miranda (Marino)
Retrieve Pistols from Campsite
It's a trap and you get ambushed. Kill the enemies and go back to Miranda. You get the option to make her pay for lying to you.
TRIGGER: Sondergaard (Marino)
Confront the Spigadoros, confront the Peacemaker, decide who you want to kill.
Reward: Buns or Maurice recruitable, nice drops
After you talk to both parties, you're free to talk either one into combat. If you side with Spigadoros, you get Maurice Chevalier from JA2UB for free for 1 week. If you side with Peacemakers, you get Buns Sondergaard. Buns is annoying, Maurice is pretty useless stat-wise. But if you kill Sondergaard he drops a golden Colt Peacemaker...
It's Just A Sexual Favor
TRIGGER: Willie (Marino)
Help Willie with his problem, go entertain Sofia, Willie's wife
Reward: 23 year old rum
Pretty straightforward quest, but Sofia only likes strong men. You need a merc with over 85 in Physique to make her happy. The 23 old rum is used in Mad Thunder Mine quest.
Every Day I'm Smuggling
TRIGGER:Fred Bearpit (Tio)
Deliver the custom rifle to Bevis
Reward: $7000 / Custom Barrett / Custom Shotgun
Fred is in Tio slums, in a shack. He sends you to Bear's Pit sector (near Gozorro mine) to deliver an unique Barrett to a strange dude called Bevis (God knows who the devs wanted to make fun there...). He also gives you a passphrase you must say (it pops up in Beavis dialogue, don't worry, just make a mental note).
If you deliver the weapon to Bevis, you get $7000. And when you return to Fred he says something about appreciating your honesty and gives you a unique shotgun. If you keep the weapon, Bearpit sends assassins after you. They're a squad of pretty well armed mercs who pop-up @ random.
Who Gave My Girl Herpes
TRIGGER: The Pimp (Tio)
Find out who gave Sandy, one of the Pimp's girls, herpes
Reward: you find out the true value of a virgin
You can go ask around everyone if you wish to read all the responses. But the true culprit is the holy man. He won't admit it unless you complete the Wine the Priest quest below.
Wine the Priest
TRIGGER: Priest (Tio)
Bring any bottle of wine for the Priest
Reward: you find out dirty things
Nowdays you find wine all over the place. Give him a bottle, get him drunk and he'll confess before you end conversion about a visit to the local brothel, solving the herpes quest.
Throwing Out the Trash
TRIGGER: Pimp (Tio)
Get the rough-looking guy out of the bar without violence (make him play chess and beat him at that). Hint: there are two types of beer in the game, he only likes one.
Reward: You will look pretty in pink
You need to give him a GREEN bottle of beer and he'll agree to a chess match. You need a merc with high INT, above 85 I think, to beat him and make him leave. The Pimp will reward you with a full set of pink armor that looks superb on Ivan...sorry... Buns.
Hungry For A Vacation
TRIGGER: Mr. Lecter, Oyster Resort
Discover what happened to Greg Hamley, check the hotel for Greg's whereabouts then deliver the meats to the bear pit and find out about a strange cult.
Reward: a free trip to Bear's Pit?
Dr. Lecter sends you on a trip to Bear's Pit with a package of meat for ther bear. You don't want to know what meat was that. When you return you discover the staff of the resort are actually members of a canibalistic cult. Follow the tips in the sector and unlock the entrance to their secret temple You should have no problem killing them all, they're all melee.
TRIGGER: Any of the 3 sisters
Secure the help of the sisters that run the lighthouses (Valeria, Violeta, Valentina)
TRIGGER: Mad Thunder Mine foreman
Find the two pieces of the secret code to OSIM base door
Reward: Cool stuff inside to recruit and equip (it will blow you mind)
After you clear the base you will find Morgan Hanley, a scientist Marion has been looking for. He's been forced to work on a secret drug for Prince that turns humans into super soldiers. You get to recruit one of these - they are nearby locked in some tubes. You can only pick one and after you picked him there's no going back so safe before you do. Explore all options of dialogue with Morgan and you will get him to confess about a secret weapon protype he's been working on, too. You'll get for free an ridiculously overpowerd .50 BMG Sci-Fi weapon, fitted as an automatic rifle, but with the damage and accuracy of a Barrett.
Destroy Flak Cannons
TRIGGER: Marion (radio) when player gets to Angetta
Reward: makes the final 3 mercs recruitable.
Kill The Prince to liberate San Hermanos!
Find a way to Angetta, kill the Prince
Reward: You win the game?
Rescue Marion before she is executed
Reward: no virgins left in Heaven for you, sorry
There are 2 mines on Garcia you can liberate and use as a source of income: Gazorro and Mad Thunder Mine. You can find recruitable characters and some tips about other quests from local NPCs.