Base Defence Systems
If you have enough space and don't mind building them, Missile/Torpedo Defences are the most cost-effective of the defensive base facilities. The odds of penetrating 12 such modules and a Grav/Bombardment Shield are 30 to 1. On average, 30 attack ships will be destroyed before one gets through. Such a system costs $3.7 million. For the same price, 3 Fusion Ball/P.W.T. Defences with a Grav/Bombardment Shield will offer only 9 to 1 protection. Each additional Missile/Torpedo multiplies your base's longevity by about 2.4, while each additional Fusion/P.W.T. module multiplies it by about 10.4. Fusion/P.W.T. defenses are more compact, however. Plasmas/Sonics and Lasers/Gauss are completely outclassed by Missiles/Torpedos in terms of cost-effectiveness.
Once aliens have found your base, they will continue to attack it until one of their craft make it past your defensive measures, and the crew are beaten inside the base. Once this happens, the aliens are content that they've done enough damage. The base defence screen is boring and gets repetitive quickly, so many players opt to not pay maintenance on defensive measures and simply allow the aliens to land. Given the advantages you have when fighting in your own base (where you have a very good idea of where the alien units will begin and what the layout is), and the fact that an alien commander is always present for you to capture, having aliens arrive could be considered more of a bonus than anything.
To minimize the chance of your bases being found, it is advisable to quickly shoot down any Scout ships on a Retaliation mission. You will need a Hyper-wave Decoder/Transmission Resolver to know what type of mission the ship is on. A Battleship/Dreadnought may show up later, but if the Scout failed to find your base, the larger ship will not know where it is either. If the Battleship/Dreadnought heads directly towards your base at top speed, you have been discovered, and you must fight.
An "optimal" base defence system might simply be a Mind Shield/M.C. Generator (to prevent aliens from attacking in the first place) and a well armed legion of soldiers (to kick them out when they do). HWP/SWS units are valuable for base defence (as they don't have to worry about psi/MC attacks), but need to be accompanied by soldiers, or attacking aliens will destroy your base by default. Defending your bases is particularly easy if you have adopted a proper base layout strategy.
Make sure you sell off excess items from your bases' General Stores periodically, to avoid the 80-Item Limit bug. Many base-defence squads have found themselves armed with 80 Heavy Plasmas and not a single clip!. In TFTD this problem is lessened since the item limit has been increased to 110 and there's a sorting algorithm preferring weapons but you can still find yourself fighting defence missions with Electroflares and other useless items (verify this).
Keeping ammo-free Laser Rifles and HWPs/SWSs on hand can reduce this problem if possible, as they are at the top of the inventory list and are distributed first. HWPs also avoid the problem of X-COM's insane quartermaster, by being automatically fully armed with the loaded ammunition... even if there is not enough actually remaining in the base! This means, for once, your HWPs are likely to have better firepower than your agents. Note however that one healthy soldier must exist in base or it will be overrun even if many HWPs are present.
Active Defence Systems
Passive Defense Systems
|Structure||Construction Cost||Maintenence Cost||Construction Time||Damage||Accuracy|
|Missile/Torpedo Defences||$200,000||$5,000||16 days||500||50%|
|Laser/Gauss Defences||$400,000||$10,000||24 days||600||60%|
|Plasma/Sonic Defences||$600,000||$12,000||34 days||900||70%|
|Fusion/P.W.T. Defences||$800,000||$14,000||34 days||1,200||80%|
|Grav/Bombardment Shield||$1,200,000||$15,000||38 days||N/A||N/A|