Starting 11/2018, forum threads about issues in unchanged parts of civil war without link to a savegame will be removed and/or ignored.

Unchanged civil war parts

Open Civil War mod changes the middle part of the civil war questline, but the initial part up to and including Battle of Whiterun, as well as the final hold campaign progress the same way as in vanilla Skyrim:

http://en.uesp.net/wiki/Skyrim:Message_to_Whiterun_(Imperial)
http://en.uesp.net/wiki/Skyrim:Battle_for_Whiterun_(Imperial)
... OCW ...
http://en.uesp.net/wiki/Skyrim:The_Battle_for_Fort_Amol
http://en.uesp.net/wiki/Skyrim:Battle_for_Windhelm

or

http://en.uesp.net/wiki/Skyrim:Message_to_Whiterun_(Stormcloaks)
http://en.uesp.net/wiki/Skyrim:Battle_for_Whiterun_(Stormcloaks)
... OCW ...
http://en.uesp.net/wiki/Skyrim:The_Battle_for_Fort_Hraggstad
http://en.uesp.net/wiki/Skyrim:Battle_for_Solitude

That does not mean issues in those parts are not interesting - after all, fort battles and minor hold city battles have as much in commom as capital battles with major hold city battles restored by OCW, so an improvement to them could perhaps apply to both parts. But you'll have to figure the issue on your own, and may this article be helpful in that.

For those who run heavy Skyrim loads (and who doesn't?), I recommend also "Skyrim Civil War: Mod Until It Breaks".

The rest of the article assumes that you are familiar with troubleshooting a regular Skyrim questline, such as the Main Quest. No radiant quests, and you are the master and commander of console commands: sqs, sqv, getqr, setstage, ... You understand the difference between quest running and quest started in journal... Perhaps even have some grasp of debugging missing quest aliases...? But certainly your expectation are that there should be a console command to override whatever glitch happened to you. Well, Skyrim Civil War questline gives no quarter, so if your Skyrim console skill is a bit rusty, it's a good idea to practice it a bit.

Whiterun: Message to, and Battle for.

Battle follows Message to Whiterun quest. A regular Skyrim questline would simply "setstage" the subsequent quest around the time of completing and stopping its predecessor. The Civil War questline starts battle of Whiterun using a Story Manager Script Event while you are still far away, and when you talk to the officer guy (Legate Cipius on imperial side, Ulfric on stormcloak side) it merely advances it ("setstage cwsiege 1" with the condole command), which starts the already running CWSiege in quest journal (actually, it is CWSiegeObj which is responsible for its quest journal).

That means you will have to reload a savegame early enough (*) in order to reattempt starting the Battle of Whiterun - unless "setstage cwsiege 1" works.

There are three most common causes of the Battle of Whiterun quest not starting up:

(a) "setstage cwsiege 1" started it! Most likely it just took the engine so long to initialize the battle quest, and if you just waited, the officer would get the appropriate dialogue line. Cases that another mod broke his dialogue are practically unheard of (but if some sloppy mod added high-priority blocking topic to all officers... you get the idea).

(b) quest CWSiege is not running, and it's not a missing alias problem - vanilla quickstart command works ("setstage cwsiegequickstart 4210" on imperial side, 4220 on stormcloak side). Perhaps the original event got stuck in Story Manager? Or Legate Cipius was loaded all the time (see (*))? Cases where another mod broke the "Message To Whiterun" dialogue/stage that sparks it are unheard of (but... you get the idea).

(c) quest CWSiege is not running, due to a missing alias - say, you used to disable annoying NPCs, including Balgruuf's kids. Vanilla quickstart does not start the battle, but ocwspecial does. More details about it at https://www.nexusmods.com/skyrim/mods/82128/?tab=forum&topic_id=6368466

If your issue turns out to be (c), consider yourself lucky. In cases (a) and (b), you may experience similar lags/glitches at virtually every step of the civil war after the battle of Whiterun.

(*) on Stormcloak side, it all begins in CW03 stage 50, that is, when Jarl Balgruuf gives you the axe. On imperial side, it begins with CW03 stage 100 (Ulfric returns the axe) and Legate Cipius gets loaded (that means, when you get back to Whiterun (Dragonsreach)... and a few more things where this process could go awry, yay!)

Final Hold Campaign

If the Whiterun had one hiccup with starting the battle, in the final hold there are two such hiccups:

(1) the fort battle - it begins when you approach the final hold military camp.

Instead of "setstage cwsiege 1", use "setstage cwfortsiegefort 10"

(2) the battle for capital city - it requires winning the fort battle (stage 9000 of CWFortSiegeFort), which sets true variable EastmarchFortBattleComplete (or HaafingarFortBattleComplete) in quest CW script CWScript. Only with that, it begins when you approach the final hold military camp.

The capital also has a cwsiegequickstart stage: 8110 for imperials, 1220 on stormcloak side.

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Appendix: middle-part glitches that may cascade into the final hold campaign

Things that in theory can prevent your faction leader from starting the final hold campaign (quest CW stage 30):

* not owning any of the other 8 holds, including Whiterun. If it's not clear from the civil war map, console command "getkeyworddataforlocation ... cwowner" can be of help; and setkeyworddataforlocation to change cwowner

* incorrect playerAllegiance (1-imperial, 2-stormcloak), inspect with "setstage ocwspecial 5", correct it with ocwspecial stages 91 and 92.

* blocking dialogue from unstopped OCW battles, check what is running (major battle quests: ocwsiegedup and ocwsiegeai, minor: cwfortsiegecapital and ocwfortsiegecapitai) and stop it