When the game starts you will need to choose a factions. Both factions can run the same heros and have generally the same Base Commanders, but vastly different abilities which can change how teams focus their strategy. Read about Factions on the Factions page.
After you have chosen your Faction you will be given a list of Ship Commanders to choose from. Of those heros only 1 is allowed per player per team and each team MUST have at least 1 Base Commander (Unless you are playing "Ships Only Mode"). Base Commanders are setup in the "in game lobby" including their corresponding faction. Ship Commanders are setup in the game on a first come first serve basis. Choosing your role is important because each hero has slightly different advantages and disadvantages. With 8 possible ships to choose from between 4 players there are a lot of combinations. Ultimately you should try to learn about the different heros by reading about them in Ship Commanders. For example, if an enemy team has alot of smaller Ship Commanders, Viper, Assimilator, Paradox, and you've done your homework, you know that the Gunstar deals 30% additional damage to those hero types. Picking the Gunstar would make an excellent choice. Or if one team had a leviathan and you know they plan to do mass swarm, perhaps you should choose the Assimilator to counter that.
Just like other MOBAs, Baseship Commanders features 3 lanes, Top middle and bottom in which minions continually spawn throughout the entire game. The minions automatically move to attack the enemy base and generally meet in the middle and begin fighting. As the game time progresses, minions will become increasingly stronger in different lanes. The object of the game is to destroy all 6 enemy Oblivion Towers located on top middle and bottom lanes. When a tower is destroyed, the minions corresponding to that tower will be stronger and push harder. The strongest and most powerful minions spawn from the bottom lanes after about 30-40 minutes of gameplay. If those bottom towers are destroyed at that point in the game the ultimate NPCs will begin spawning. At the beginning of the game, players will take their chosen Ship, or Base Commander, and begin moving out to the middle to farm minions (Kill them). Farming is important throughought the entire game because it provides both minerals and experience which you will need to purchase upgrades, unlock your augmentation, and use faction abilities. Additionally, you earn more experience and income by killing other heros, but the more you kill, the more you increase your own bounty as well. While farming you will encounter the enemy ships and choose when to engage in combat and when not to. Knowing when to stay back and play it safe is just as important as knowing when to strike.
Ship Commanders get to choose 1 of 3 powerful augmentations that are unlocked after they have earned 12,000 experience points. These augmentations can modify a Warship ability, weapon system, or passive buff giving them a strategic advantage in that area. There are many possible builds with augmentations when combined with upgrade queues. You can read about Augmentations in Ship Commanders.