Players can choose to engage in a variety of space and atmospheric combat missions using one of nine spacecraft. Each starfighter carries a certain combination of weapons. The player earns money for killing enemy targets or completing missions, which vary from simple intercepts to escort duties. The money earned can be used to buy more advanced spacecraft and weapons. Although the spacecraft have a certain combination of weapons, the game introduces an upgrade system where players can insert new weapons and parts into a number of predetermined slots on the vehicle. However, there are limitations: the player cannot install more than three of the same kind of laser. These parts can include scatter guns, subspace dampeners, and drones of various purposes. The velocity sight used in Vengeance also returns.
When fighting any large space vessels, the player is now given a chance to target individual parts of the ship, such as gun turrets.
Compared to the more linear structure of the first two games, Red Sun incorporates a more 'open world' structure with increased role playing elements. Since the player is a mercenary, a number of missions are arrayed in the Status Menu for the player to choose from, but only those marked with the letter P must be finished to advance the plot of the game. Engaging in non-story critical missions allows the player to earn money and purchase ships and weapon upgrades to help progression through the main campaign.