Start by asking yourself a series of questions. For example - you write:
“you are supposed to fight your way through a mineâ€
In this scenario, who are “you� Be specific in your mind even if you don’t include all the details in your game, age? gender?, race?, do you have a family?, do you live near the mine?
Why are you fighting your way through this mine and not someone else? Were you chosen in some way (if so, by who and why) or did you volunteer (again, why)? Have you ever done something like this before? Are you an experienced warrior facing danger with fearless determination, or a timid novice, terrified but eager to prove himself? You might be using randomly generated stats and/or allowing the player to chose some of the details of the character. This can make the player feel more involved, but it can also limit you creatively. Either way you should still have a lot to work with.
You refer to the “evil†that is poisoning the well. What or who is this evil? Why is it doing this? Is it just because it is “evil�, or is there a more concrete motive? Have you ever faced this particular evil before? You might reveal these details at the beginning of the game or make the player discover them as they play, making it part of the game. But however you do it you should know them before you get to far in so you can drop hints, foreshadowing, back story etc.
You talk about poisoning the water. What kind of poison and what effect does it have? Does it just kill people? Does it kill them quickly or slowly? Does it make them sick?, if so what are the symptoms? Or it might be a mystical poison that infects people with “evilâ€. Or it could turn them into monsters or zombies or something like that. Is there a cure/antidote? If there is, is it given to the hero or is it something you need to discover?
Just some random thoughts that I hope help you in someway.