The most important structure! You should be building them every time the cooldown is refreshed. Each Factory produces 7 minerals per second.
The second most important structure! While not as critical in the early game, you will find yourself starved for gas in the late game if you did not build enough of them.
Repair and Research Center
The Research and Repair Center acts as a Base Commander extension, generating a healing and research aura and also allows the Base Commander to upgrade every aspect of their base defense and abilities.
The Repair Center and the Base Commander cannot heal shields. Thats where shield Generators come in handy. In addition to healing shields rapidly, the Shield Generator drastically reduces all incoming damage to all nearby units and structures inside the shield
Alien Particle Accelerator
The Alien Particle Accelerator can solve any energy crisis for Ship Commanders! Definetely worth the cost if you have Ship Commanders with high energy demands.
The bread and butter defense of the Base Commander, capable of attacking both air and ground with high damage outpout.
Powerful anti-air cannons. Stronger in greater numbers, flak cannons ignore armor and have far greater range then beam towers making them an anti-ship commander necessity.
50% of damage dealt to this tower is automatically dealt to the attacker, regardless of its position making this one of the most useful base defense towers against special range weaponry and abilities.
The Quantum Laser Drill can only target enemy structures at a range of 10. Unlike other structures, the Base Commander has to be within a range of 10 to build this structure so it is best used as an offensive tower push with an emergency shield.
Siege Fortresses have no range limit and can lay waste to the enemy Base Commander and structures. While the Cooldown is relatively long in between a bombardement, if the Commander researches auto-targeting, they will gain the ability to have continous fire making them one of the deadliest offensive weapons available to the Base Commander.
Fighter Hangers launch fighter swarms at nearby enemies. Additionally, it produces Strike Bombers which can be launched from the hanger to attack enemy Base Structures. Strike bombers are stronger when launched in swarms, especially after using ion cannons to disable the enemy defenses.
Ion cannons have no range limit and can target any enemy structure (except the Base Commander) disabling all of its weapons and systems for 30 seconds. Ion cannons are best produced in mass quantity, as the Base Commander can use the Ion Cannon hot key to select all Ion cannons and fire multiple blasts disabling key structures when needed.
For the training of troops and the building of armies, the Merc Compound allows the Base Commander to build an army if he/she so chooses. Additional upgrades can be found within the Merc Compound submenu.
The ultimate in anti-ship commander defense! These gigantic missile turrets are so massive and deal so much damage at huge range that they require the Commander to research them before building. Obliterator Turrets have 2 modes, Assault and Artillery. Assault is useful for smaller faster ships while Artillery is useful for larger slower moving stationary ships, such as a sieging destroyer.
Offensive and Defensive Structures
Missile Silos are capable of attacking both air and ground. Ballistic Missile Strikes fire a smaller Nuke capable of dealing up to 500 damage in the AOE area and EMP Missile Strikes disable an enemy air units weapon systems for 10 seconds. When combined with other defensive structures, and Strike Bombers, Missile solos can be a handy defensive and offensive tool in the Base Commanders belt.
Anti-Missile unlike their counterpart, are designed to automatically detect and intercept incoming missile strikes. Any Base Commander planning to do long range missile strikes should protect his own from certain destruction by building these frequently. Not only can they intercept Destroyer's Nuclear strikes, but they are also capable of intercepting EMP Missile Strikes with a range of 60.
Power Modules can only be built by the Ancient Imperium Commander. Power modules act like a stationary Base Commander and provide free power to base defense structures in addition to cloak detection.
With the increase in Base Commander offensive strategies has come the need to hide certain key structures from the minimap. Enter the Radar Jammer! capable of hiding even from sensor scanners, any units inside of the Radar Jammer can only be revealed by an approaching unit. This makes Radar Jammers one of the only defenses against Ion Cannons and Bomber runs. (Does not hide Oblivion Shrines)