Expeditions: Conquistador is a turn-based tactical RPG where players taken on the role of a Spanish explorer arriving at the island of Hispaniola in the year 1518. The game has two campaigns: Hispaniola and Mexico. The goal of the Hispaniola campaign is to mount an expedition to Mexico, where players will encounter the Aztec Empire and face the choice of whether to ally with the Aztecs against a tribal rebellion, to ally with the Totonac tribes to overthrow the Aztec Empire, or play along with either side until an opportune moment arises to turn on their allies and take Mexico for the Spanish crown.

At the start of the game, the player selects their gender and name, and assigns points to six statistics: Tactics, Diplomacy, Healing, Survival, Scouting, and Leadership. Then, the player selects 10 expedition members from a pool of 31 pre-written characters with unique portraits, biographies, and personality traits. The gameplay is divided into two parts: on the overland maps of Hispaniola or Mexico, the player's expedition is represented by a conquistador character on a horse. Here, the player can ride around to explore the game world, encountering events and picking up resources. The expedition can move a certain distance each night before they have to make camp. This opens up a camping system where the player must assign tasks and rations to each of the expedition members, treat injured followers, construct items to be used in combat, or research upgrades for the expedition. Camping (as well as travelling) will also trigger random events such as conversations with the expedition members, ambushes, and so on.

Events are text-based (accompanied by hand-drawn 2D illustrations), but often they will trigger a battle. Like the overland map, the combat system is turn-based, with the player controlling up to 6 units at a time, typically against a slightly larger group of enemies. Each side gets to move all their units in any order they please before ending their turn, and each character can move and attack in any order, which allows for advanced tactical manoeuvring. The game has 10 different unit types. On the Spanish side: Soldiers, Scouts, Hunters, Doctors, and Scholars. On the native side: Warriors, Trappers, Shamans, Champions, Amazons. The player will also sometimes be fighting native Civilians. Each character class has up to three active abilities (depending on rank) plus two special abilities for officers. When players promote a unit, they can also select a passive ability that will give the unit certain advantages under certain circumstances.

Battlefields are hex-based, but unlike many hex-based games of this type, every battlefield is hand-made and always relates to the story of the event that it is part of. The victory conditions, starting positions, etc. of each battle likewise depends on the story, and often changes based on the choices the players made in the event that led to the battle. Any unit who was incapacitated during a fight may get an injury that carries over into the overland map, which has to be treated using medicine when the expedition makes camp. An injured unit cannot be used in combat and will not be able to carry out tasks in the camp.

The game has 5 different storyline endings with variations depending on the state of the expedition at the end of the game.

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