The mission system and gameplay related to space. (Yes, there are other locations and mechanics.) Part one.
First, to make this easier to understand, remember that access to the game is divided into paid and free parts. A player with a paid account also has access to all free mechanics.
It's also worth saying that completing missions isn't required for progress in the game. They're primarily entertainment and an aid to development.
1. Military-command missions. In these missions, the player takes part in military campaigns conducted by different species in star systems. Each species has its own hangar, base of operations, statistics, selection of ships, and crews. The player can play as every species. According to the situation, the mission generator and/or commander provides a list of assignments in which the player can participate. Missions take place both in instances and in real space, sometimes very far from the human sphere of influence. Available missions are determined by the player's rating with the particular species or by the commander's decision. Rewards include a higher rating and development points, which can be spent on ship improvements, crew training, and access to new ships. They can also be converted into intelligence, influence, and sabotage points, which are very useful to players with paid accounts. Players with a high rating for a species may gain control of an entire military operation and assign missions at their discretion.
1a. Human missions. Their tactics differ somewhat from the others. Human military command uses unique technology that, with certain limitations, can project its ships to any point in space and return them to their origin afterward. This determines the style, tactics, and nuances of combat. Only what was projected returns, so nothing can be moved from the destination back to the starting position. The advantage is that even ships that have completely lost combat capability and control return and can be repaired. Whatever the outcome, the battlefield remains in enemy hands, so neither side receives trophies.
1b. Missions for other species. These follow a more traditional style. Trophies can be obtained, but losses in defeat are permanent. Since players act as commanders, however, they'll always receive ships. The question is only which ships, and that depends on rating and development points spent on equipment, skills, connections, and so on. A player may own captured ships and use them in missions as they choose. They may also use their own personal ships in missions, though that applies to players with paid accounts.
2. As already mentioned, missions may also take place in real space and affect players with paid accounts and their property.