The ally system allows you to add Facebook friends and in-game friends to your game. You can get crystals from achievements by having a certain amount of friends. The maximum amount of in-game friends you can have is 50.
Facebook Friends x10 FB Friends:100 Crystals x20 FB Friends: 150 Crystals x30 FB Friends: 200 Crystals x40 FB Friends: 250 Crystals x50 FB Friends: 300 Crystals You can get 1000 crystals by having 50 FB friends in your game.
In Game Friends/Allies x25 Allies: 50 Crystals x50 Allies: 100 Crystals You can get 150 crystals by having 50 allies.
Allies and Facebook friends can send each other Assemble Points. Assemble points can be used to buy energy and assemble boxes. The maximum amount of Assemble Points you can get per day is 1500.
You can recharge 25 energy by spending 500 Assemble Points, but you can only buy 3 per day.
You can also get Assemble Boxes for 300 Assemble Points. You can draw various awards such as gear upgrade items, biometrics, etc.
In missions you can select an ally to help you out in missions. To the right of your screen you should see their character or Facebook profile pic if it's a Facebook friend. When you click on that, their character goes in for 10 seconds and fights the enemy with you. However, you can only use them once in that battle so it is recommended to use them during boss fights. There is a recharge time of about 25 minutes for allies that have been selected for a mission.