Attacking and Defending
During your Main Phase, you may declare an ally as an attacker. Only unexhausted allies that started the turn in play may attack. (You cannot attack with allies you just played.)
During your opponent's Defense Phase, they may defend against attackers with any unexhausted allies. Defending causes the defending ally to become exhausted. Attackers may be defended against multiple times. When defended against, the two allies battle.
During battle, both allies deal damage to the other equal to their attack points (AP). If this decreases an ally's HP below 0, it is destroyed.
At the end of the Defense Phase, any remaining attackers will deal their damage directly to the player.
Damage is permanent while an ally remains in play. This means that a 2 AP / 3 HP that takes 2 damage would permanently become a 2 AP / 1 HP. Some ways to reverse this damage include: using a card that heals allies, or returning the ally to your hand and playing it again.
The Bench is a game zone where cards are placed face-down. You can see your own benched cards, but not your opponent's benched cards.
Benching cards can be thought of as pre-playing them. Like playing, it costs energy to bench a card, however cards can later be played from the Bench without repaying their energy cost. Additionally, allies and objects can be played from the Bench during your Defense Phase (they normally can't be played from your hand during your Defense Phase).
Trap cards are used from the Bench, rather than in play. They trigger when some game action occurs, and then are placed in the graveyard. For example, Trap Spider triggers when your opponent attacks by giving you a new spider ally.
Once per turn, you may discard any card for one energy of its color. This is called converting the card into energy. Generic (gray) and multicolored cards are converted into one generic (gray) energy.
You must pay a card's energy cost in order to play it. Fortunately, generic (gray) energy costs can be paid with any type of energy, not just generic energy. Colored energy costs, however, requires colored energy.
For example, if you have 1 green and 1 red energy, you can play a card that costs 1 green and 1 generic energy, but not a card that costs 2 green energy.
Your energy regenerates at the beginning of each turn. For example, if during each your first two turns you discarded a yellow card for energy, then you will have two yellow energy at the beginning of your third turn (and all subsequent turns). As the game progresses, you'll be able to afford more powerful cards.
Phases of the Turn
Turns are composed of a Defense Phase and a Main Phase.
At the beginning of your Defense Phase, your energy regenerates and you draw a card. During the Defense Phase, you can do one of four things: defend against any attacking allies, discard a card for energy, use the ability of a card in play, or play an action card from your hand. Note that you cannot play allies or objects during your Defense Phase.
At the end of your Defense Phase, you take damage from any undefended attacking allies equal to their attack points (AP).
At the beginning of your Main Phase, after your Defense Phase, all exhausted allies you control become unexhausted. During your Main Phase, you can play any card, use any ability, and declare attackers.
When you are done with your Main Phase, click the "End Turn →" button on the right-hand side column. It'll then become your opponent's turn.
Each card is made up of various components: name, color, type, subtype, energy cost, card text, and, in the case of an ally, attack points (AP) and health points (HP).
You can't simply play any card you like. First, you must be able to afford its energy cost. Second, cards can't always be played, depending on the phase of the turn.
During your Defense Phase, you can only play action cards from your hand, but not allies, objects, or traps. However, any card can be played from the Bench during your Defense Phase. This gives you an the element of surprise, if you plan ahead.
During your Main Phase, you can play any card that you have the energy to afford. A few cards require additional conditions in order to be played, such as having played at least two cards that turn.