Choosing Sides
It doesn't matter which side you choose as they both pretty much play out the same, it's just a matter of what base buildings you prefer and whether you want to be the good or bad guys.
Building Log
Focus your attention on the recommended missions in the building log as the rewards you will recieve for completing these will make sure your base is heading in the right direction.
Invade
Although you do not have direct control over the troops you've built it is important that you send them out to capture resource points to gain the necessary supplies to strengthen and build your base.
Train Troops
Make sure your boot camp queue is never empty and that you are constantly training a different variety of troops as more often than not you will be able to resolve conflicts by just having superior numbers of them.
Correctors
Once you have accumulated enough firepower you can earm valuable trophies that provide you with a lot of boons by scanning the wastelands around your base and taking down in incremental attacks the giant invading robots called Correctors. Keep in mind that you will need to wait for your attack charge to replenish before you can attack a Corrector so make the most of every opportunity.
Research
It is important that you research whenever possible as doing so enables you to get stronger troops which will imporove your chances of capturing resources.
Missions
There are three types of missions, these are personal, strategic, and clan missions. Make sure you have missions running whenever possible so you are able to collect the rewards when these time-based tasks that don't require you to do anything have completed. If you set off a long mission just before you put the game down you will be able to pick up the reward the next time you log in.
Rewards
Don't forget to claim your rewards as some of them are well hidden in the UI and can be easily missed. Make sure you check everything with a notification dot next to it to ensure you have picked up everything you are owed.
Avatar
Tapping on your character portrait will allow you to access options that will make them more effective and if necessary change your leader.
Skill Tree
You have two different sets of skill trees, one for your base and the other for combat and you get separate points for each of them. For a skill regardless of the set to unlock to the next tier of the trees you need to upgrade it fully it is important that you consider this when you spend the points you have earned.
Clan
A great way to increase the boosts and resources you recieve is to join a clan. Even if you have no interest in playing with others it is worth doing as the bonuses you get will help you out immensly.