It is important that you keep your morale above 50. If it drops to 50 and below, the player's stats will be negatively affected largely. A way to prevent morale getting to low is to rest at the hospital, or buy a mushroom. Mushroom gets you 40 condition back.
You lose morale for not completing goals from Captain or anyone else from the team. The easiest way to lose morale is to train too much or do too much part time jobs or voluntary work. Low condition can also result in illness and injury. Be sure to keep your morale up!