Fleet Commanders are available from Ops 15. They are stationed at your station's Command Center. You cannot put them on a ship crew or send them on Away Missions. A seated Commander gives fleet-wide buffs in combat, economy and ship work. Examples: Phase Bank Upgrades (more Energy Weapon Damage), Alloy Metallurgies (cheaper Tritanium ship upgrades) and Unimatrix Training (more damage against Solo and Group Armadas). Choose Kirk or Spock as a free unlock through a mission. Every other Commander comes as shards from daily gifts, events or the Offers tab. Once you can build the Vindicator, you can also claim daily shards for other Commanders.
An Active Ability is a fleet-wide effect that you trigger yourself. It is stronger than an ordinary passive buff. A cooldown limits it, so it is live for only a few minutes at a time. It only works if that Commander sits in the First Seat, the leftmost Command Center slot. Owning the right Commander is not enough if they sit in another slot. Upgrading or leveling the Commander lengthens the active time and shortens the cooldown.
Benjamin Sisko is built for Outpost combat and loot, with value in general PvE and PvP too. You can get him from day one through the Outpost Refinery. His Active Ability repairs up to 25% of Hull Health on your ships fleet-wide. It does not affect ships already in combat. Much of his kit applies only to Federation, Klingon and Romulan Grade 5+ ships. He is a stronger pick if those ships are the core of your fleet than if you fly mostly Independent or faction-specific hulls.
Sisko has three skill trees. Tactician is mostly always-on buffs. It raises Isolytic Damage against non-Armada hostiles for Federation, Klingon and Romulan Grade 5+ ships, raises base Hull Health for those ships, adds a very large Weapon Damage bonus against Outposts and their Retaliation hostiles, and holds his Active Ability. Combatant leans PvP. It raises Shield Health for the same three factions and adds large Apex Barrier bonuses against players, some of them under conditions (Morale, Hull Breach, Burning). Mechanic is the economy tree. It boosts Cargo capacity, Mining Rate, positive reputation gained from Federation, Klingon and Romulan hostiles, Solo Outpost Credit and Component loot, and Outpost Fleet Size. That last one lets you field one extra ship in every Outpost engagement.
Gabriel Lorca was the Fleet Commander who introduced the Active Ability. His ability is a time-limited fleet-wide damage buff. You unlock it at Combat Tree level 5.
Khan Noonien Singh is built mainly for PvP. His buffs help in PvP combat, Arena and Station Defense. He also helps when mining with Surveyors and adds PvE value by raising Apex Shred against non-Armada hostiles. He has three skill trees (Visionary, Extremist, Overseer) with critical damage, critical chance, Apex Barrier and Shred, and Isolytic Damage and Defense. His Active Ability, Wrath of Khan, gives a large temporary critical damage boost. You can earn his shards free through Khan Quests. These are special, high-value Priority 1 Away Team Assignments from the Away Teams Research Tree. You can also earn them by defeating the Champion hostiles added with the Augment Faction expansion.
At Ops 15, claim the Legends of the Cosmos mission in the Holodeck. It gives the 18 Quantum Communicators you need to build the Command Center. After the mission, claim the remaining Fleet Commander shards in the Refinery (Command Center tab). Quantum Communicators also upgrade the building. Seat 1 is open at Command Center level 1. Seat 2 opens at Command Center level 40. Seat 3 opens at Syndicate level 40, and seat 4 at Syndicate level 65. Seats 5 to 7 are Store offers. Seat 8 opens through the Outpost Refinery at OCC level 61. Dock all ships before you change Commanders. The 30-minute timer is only a swap cooldown, so buffs stay on while a Commander is seated.