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The fiction I write currently hit a major snag and needs a big overhaul of a major part of the story. A whole, large thread is being injected, a second conflict running in parallel with the main one and nearly as big - maybe smaller scale-wise but possibly even more complex.

Thing is I have a big part of the story according to the old, single-threaded paradigm is already written. Most of it will be reused in almost unchanged shape content-wise, but will require serious edits on the "details" level.

...and with my experience from programming, adding a second, distinct functionality to a pre-existing module with one existing functionality creates much, much more bugs than writing this from scratch separately.

I'm afraid my old story will be full of plot holes, pieces that depend on past that's been changed, on time-space relationships that are no longer valid, on knowledge that due to certain events became available or got lost in the changed version.

For example: when before there was just the dark clouds on the horizon, there comes a whole new layer of plot and subterfuge, opponents at hand, observing the protagonists from the shadows. They will not hesitate to strike at any open vulnerabilities. Suddenly all (common) scenes where the protagonist just didn't care about immediate danger (because there was none) need to either excuse the opponents from striking at the exposed character, or provide some defense, or just turn into battles. Any moments where I leave the protagonist just exposed, and nothing bad happens, as he is most of the time now, become plot holes.

So, are there any trusted techniques to trace such dependencies, and hunt all plot holes depending on changes of the story? Trace locations, knowledge, items to make them end up where they are? Like, in the old "Wolf, goat and cabbage" riddle, introduce a chicken and a sack of grain, and still reuse most of the old solution?

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The best thing is to get someone else to read through what you have. I find it difficult to look past the changes, because I know what was "supposed" to happen before the change. Someone who is unfamiliar with your story will be better situated to go through it without preconceptions.

There's something to be said for doing this yourself. It's amazing how well just saying to yourself, "I haven't read this before, I have no idea what's going to happen," works.

I am also a big fan of drawing out a timeline of events. Where was Bob when X was going on? Why didn't Alice show up at Y? Could Charlie have realistically gotten from here to there in the amount of time he had to travel? Putting every event on your timeline will help you keep your characters, your events, and your plot on the straight and narrow.

Finally, I wouldn't necessarily worry about filling in every single perceived plot hole you find. As much as the IT folks like to scream, "Security through obscurity is no security at all," sometimes people don't exploit a weakness because they don't see it. So your main character is standing exposed and no one takes a swing at him. So what? Sometimes the bad guys just don't notice. If it helps, you can seal up your plot hole by pointing it out. "Daniel stood in the field of battle, blinded by sweat and exhausted by the effort of simply standing. Had anyone chosen to attack at that moment, he couldn't have fended them off with more than a stern expression. Luckily, though the battle still raged, no one approached and the moment passed..."

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I'd use a spreadsheet as a wireframe.

If you don't have such notes already, you may have to examine your story a section at a time, and make notes about each part detailing what's going on with Plot A. Then use the spreadsheet to make notes about weaving in Plot B.

The advantage of the spreadsheet is that everything is modular, visible almost all at once, and very easy to move around.

It may be necessary to go over your book several times to fill in all the spreadsheet gaps, particularly once you actually start writing and you find threads which suddenly dangle, but using a verbal wireframe will make it much simpler to see where all the variables are.

Then find a really good editor and explain what you've done, so the editor knows to look for plot holes.

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    I'd only add to this that you be careful how granular you get when deciding what elements to add to the spreadsheet (or mind map, or post-its with string on a corkboard). Pick a system - say, major events in each plot thread, etc - and stick with it. Sweat the small stuff only later, when you go through and do a cleanup after hitting the major stuff. Commented Mar 20, 2013 at 3:52
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I find mind mapping programs like Freemind or Freeplane to be especially helpful with sorting out continuity and plot devices. Nodes can be formatted with different fonts, borders, colors, etc. to visually separate different components of the story.

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