The player is the Emperor and there is a storyline about a conspiracy to overthrow the emperor. There are other storylines as well, so it's not about this particular storyline.

Now, the player gets storyline related events and has an option to PROGRESS the storyline (uncover the conspiracy more). Once fully uncovered the storyline ends (which is good and desired).

Based on what is the state of the PROGRESS the player gets new events related to this storyline.

So far it's all perfect, but how to handle the progress of conspirators (NEGATIVE PROGRESS)? They should attempt assassinations and the like, if the player takes too long to uncover the truth.

So, how to make it? In a typical linear storyline you go forward and then bad things happen (so positive and negative progress is tied together, these are one, just like reading a book), but I can't (and don't want to) do it this way here. At least I have to assure that progressing the storyline (uncovering the truth) is ALWAYS benefitial and desired. While neglecting progressing it should be undesirable and be punished by the game.

So,

Essentially, you want them to continue the story so your work is seen and the plot is pushed forward, but you don't want people to neglect the story, since that would mean you spent time on a feature that won't be fully appreciated?

Right then,

So, all you do is take the choice out of the game.

Sure, a bit drastic, but given all the posts and effort you've put into the game already, there is no way the game will continue if the emperor is successfully assassinated.

(If you do allow this, it could actually make an interesting twist, meaning, you have to start over with your re-cloning of the precious emperor, forcing the player to losing time.)

Doing that would have your empire fall into disarray, and cause wild card variables to potentially pop up.

Or,

Did you mean, that's what you don't want, negative story events actually having an effect on the game play?

If so, I go back to saying, take the choice out of the game, and it just being a play along adventure.

The issue your trying to face is how to minimize the effect of the story on game play, the fact that you didn't start your design as story as a core component is forcing you to bolt on a story after most of the mechanics are already in progress or done.

(it's common, but holistic design requires having this game play vs. story balancing act way earlier in development.)

Best advice?

Either remove the story, and focus on your mechanics, or make the story a linear experience, those are the cleanest options you have at this point.

The fact that you don't want or can't make the story to actually impact the game, makes most of your other story efforts largely irrelevant, and nothing more than fluff. (if that is indeed the case)

Going on about an immortal Clone emperor means little when you have no intentions on showing clones. Why not just make your emperor an AI?

Sigh,

I don't mean to be this negative, but what do you expect if you don't want the story to impact game play at all?

It makes developing a story totally frivolous.

Your asking us how to give the player an illusion of choice, when there is no choice, and instead of spending your time trying to figure out how to fool the player, you could just scrap the dead weight, and polish your core mechanics more.

It's clear "story" won't be a "selling point" of your game, evidenced by the mere fact you continue to outsource seemingly all vaguely related story points to this forum. Thus, it might be better to focus on your strengths, instead of half assing a story, just so the player has more to think about than managerial concerns.

The best thing I could think of is a linear storyline with (POSITIVE) effects that is driven by the player and separate (NEGATIVE) mini plots triggerred by time. So, the storyline (uncovering the conspiracy) can be progressed by the player without any bad effects in a linear fashion while based on the game time NEGATIVE disconnected subplots are triggered on regular intervals (like consiprators making a move to bribe someone near the emperor, or make an assassination attempt). The NEGATIVE plots will cease to trigger if the player ended the whole storyline (uncovered who was the culprint and eliminated the threat).

Does anyone have a better idea?