Every post-searing Cooperative Mission in the Prophecies campaign has a Bonus Mission. The bonus is added to your quest log when you acquire it. Bonus mission objectives are obtained either at the start of the mission or while playing through the mission, but it is not guaranteed that you will find the bonus. It's quite possible to finish many missions without knowing what the bonus was, unless you search the mission thoroughly. You get 1000 experience when you complete a bonus, and sometimes receive additional rewards.
Canthan Cooperative Missions have two possible bonuses. Expert bonuses give you an extra 1,500 XP, a skill point, and 150 gold in addition to the normal reward. Master bonuses give you an extra 2,000 XP, a skill point, and 200 gold in addition to the normal and expert bonus. For all but two of the missions, the bonuses are rewarded according to completion time of the mission. For the Gyala Hatchery (mission) and The Eternal Grove (mission), the bonuses are dependent upon keeping NPCs alive throughout the mission.
Elona Cooperative Missions also have a three-tier completion system, similar to that found in Factions. All mission bonuses in this campaign have a multi-level bonus. They could consist of doing tasks, killing bonus monsters, or completing the mission within a set amount of time. The rewards for achieving the bonus are as listed in the Factions campaign above.
It should be noted that time 'freezes', and minions don't lose health, during cinematics. This means that players can watch the cinematics without fear of losing the bonus.