Plot in your Sandbox Campaign

The nature of a roleplaying game means that the players are always doing unexpected things. Where the referee creativity comes in is planning out the consequences of what the players given the circumstances and the NPC's motivations. Not in writing a story that the players ride along with.

It doesn't matter what the results of the encounter is before it happens. What important is afterwards when you decide how the NPCs and the environment react and change.

A Story Arcs needs to be Plot Arc and it is a plan of action that will change after the PCs interact with each encounter. Think of your setting, NPCS, and locale as a bag of stuff. What mix get put out depends on where your PCs are, and what they did. With this you don't have to worry that a specific outcome must occur at a specific time.

The easiest way of planning the plot is to think of it as series of What Ifs. What if Darkon the Lich gets killed here, what if he survives? While it appears to be daunting in practice these What Ifs turn out to be limited. The interests of the players, and how they play, are strong clues as to what they would reasonably do. You can use this knowledge to manipulate the players as well to narrow the range of possibilities you have to prepare for.

Not everything is fluid either. For example if you had an volcanic eruption planned for two months into the campaign then it will generally go off. It going to be your call as to which part of the plot's timeline is like this. Also no wins are fine, if the players have plenty of warning.

If two sessions into a 13th century medieval Europe campaign, they decide to go and get Genghis Khan's head then it going to be highly probable it will be the PC's heads that will wind up a heap. But the saving grace of the situation is that likely the PCs will hear about the size of Mongol army and the nature of the Khan's guard well before they get to the point of no return. Put out the information and if they ignore it, let the dice fall where they roll.