Your base allows you to create one platoon specifically for the purpose of base defense. These Base Defenders will deploy automatically when your base is attacked and will fight to the death to defend it. You only have one base defense platoon, so your Base Defenders will often be outnumbered by invading forces, but you'll also have the benefit of your defensive structures, so the Base Defenders aren't your sole line of defense.

To add units to your Base Defenders platoon, simply click on your Storage building and look for the Open button.

This brings up the Platoons window:

Your Base Defenders platoon is over there on the left. Currently it's empty, so the game tells us our base is undefended. We need to add some units to that platoon, so click on it. You will then see the option to Manage the platoon. Click on that option (seen below).

Now you should see this window, which shows you all the units you currently have in Storage that are eligible to be added to your Base Defenders platoon (not all units can perform all duties). 

Click on a unit type to add a unit to the Base Defenders. Each time you hit that green arrow, it will add a unit of that type to your platoon (until you run out of that unit type or reach your platoon's capacity, anyway).

As you add units to your platoon, keep an eye on the capacity of your Base Defenders platoon (it's there towards the bottom of the window, as indicated by the left arrow in the screenshot below). Each unit in the game has a size value; you can put any combination of eligible units into your platoon, but the platoon's size is limited by its capacity. The capacity of your Base Defenders platoon increases as you level up your Command Center:

Once you are satisfied with the composition of your Base Defenders platoon, click that Save button. You're ready to defend your base!

Some units in the game are better suited to defensive duty than others. Over time you will definitely want to research some of these specialized units for use in base defense; they will add greatly to your defensive firepower and make your base a much harder target.

Another way to harden your base defense is to upgrade your Defense Lab. Your Defense Lab lets you research lots of cool defensive turrets (more on that later...), but from level 11 onward, it also reduces the amount of damage your Base Defenders take in combat! The Defense Lab reduces damage taken by the Base Defenders a fixed percentage based on the Defense Lab's current level. This reduction is not cumulative per level; this table shows you the total damage reduction as determined by the Defense Lab's level.

The Go-Go Bar also provides a couple buffs for your Base Defenders. Depending on its level, the Go-Go Bar increases the amount of damage done to attackers by your Base Defenders, and reduces the amount of time it takes to repair them. As above, these bonuses are not cumulative; the number shown here is the total bonus at the indicated level.