Indigo Prophecy is all about the choices. Pretty much everything you do will affect how characters will act (and consequently how scenes will play out) later in the game. Simple choices like washing the blood off your hands will leave evidence in the sink, but allow you to make a cleaner getaway (no pun intended).
But I guess I should explain the situation some before I get too ahead of myself. Indigo Prophecy follows two sides of the same story. One side follows Lucas Kane - a person who, for some reason unbeknownst even to him, has just murdered a total stranger in a diner bathroom. The other side of the coin follows Carla Valenti and her partner, Tyler Mils, who are looking for the murderer (Lucas).
From the first instant you gain control in this game, you are presented with choices. You start off as Lucas, standing over the stranger's body with blood on your hands. You know you need to leave the diner, especially since there is a cop sipping coffee at the counter and he is bound to need to relieve himself eventually. So what kind of choices do you have? Do you hide the body? Clean the blood off the floor? Clean the blood off your hands? Hide the murder weapon? These are just a few of the choices that can affect what the investigators (Carla and Tyler) may or may not find later. And those are just the choices in the one room -- you haven't even left the diner yet.
As I said, at its heart Indigo Prophecy is a murder mystery, but you are both the murderer and the cop. Because of this, you might hide evidence (or try to) or later find evidence that you didn't even think you were leaving behind in the first place. This makes the game an unusual cat-and-mouse situation where you are both the hunter and the hunted. Of course, both sets of characters are trying to find out what is really going on. Lucas is just the only one of the three that knows something unusual is going on.
One of the many interesting aspects of Indigo Prophecy is that many of the events take place at the same time. For instance, while Lucas goes to meet with his brother early in the game, Carla and Tyler will be at the police station. When these simultaneous events happen, you will be given the choice of which character to play as first. When these choices appear, which character you play as first doesn't affect how the other character reacts at that time -- but it may and will change how things will play out later. Basically, if in the above example you choose to play as Lucas first and you succeed in convincing your brother to side with you, it won't affect what Carla does in the same scene, but it might have a bearing on what Marcus (the brother) does later.
On top of everything else -- you also have to be mindful of your characters' mental health. As your characters find clues (or hide them if you're Lucas), their mental health will increase because they will get less anxious. But if Lucas hears about the murders or remembers something tragic about his past, he will start to get depressed. Likewise, if Carla or Tyler get tired or have a fight with another character. Even actions like drinking alcohol will affect the characters' mental health. Typically, the first swig (if it isn't taken with meds) will increase his/her health -- while each subsequent mouthful will drop them closer to depression.
