The After Dark penalty is in the game to allow players some "relax time", a time of day when they do not need to worry quite so much about the threat of attacks from other players. As such, from 00:00 to 08:00 server time every night, all attacks have a 40% penalty.
For the two hours on either side of these times, the penalty will ramp up to, and down from, the full 40% penalty:
The After Dark penalty affects all attack types (scout, plunder, assault and siege), and also affects building and fortification damage, as well as senator siege claims.
The After Dark penalty is only applicable for PvP attacks, and will not affect cavern or boss raids.
In order to stop large players "farming" small players, there is a Morale penalty in the game.
If an attacker is more than 5 times the empire score of a defender, a morale penalty is applied to the attacker, according to the equation (attacker_score/defender_score)*10
Some examples of Morale penalties:
The maximum morale penalty that can be incurred is 500%.
When a player is attacking through a portal, the farther his troops travel from their home city, the greater a penalty will be incurred. This does not apply to reinforcements. For more information on the portal penalty, see the Portal page.