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I've completed the Civil War questline in the Empire's favor in one game. Since then, I've noticed several indicators that Talos worship still hasn't been as thoroughly eradicated as one would have expected. One strong indicator of this is that Heimskr seems to be allowed to continue preaching in Whiterun. Other examples are the continued existence of Shrines of Talos in Markarth and Riften. One might expect these to still remain in the wild somewhere, but not in major cities.

Is there any canonical explanation for this?

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Also, the Temple of Talos in Windhelm is still open to Talos-worshippers and is still attended by its priest and priestess after the Imperials take control of Windhelm. – galacticninja Feb 4 '12 at 14:41
I think this might be a plot hole. – ヴァイシャリ Feb 14 '12 at 16:13
It's due to a bug. Heimskr was actually supposed to be sent to jail if the Imperials win the battle, but a bug prevented that from happening. – galacticninja Dec 1 '12 at 5:40
up vote 5 down vote accepted

According to some NPCs, the real reason for the Thalmor "witch hunts" is the bravado with which Ulfric & Co were professing their faith, and before that the worship of Talos wasn't actually persecuted. Perhaps the Empire is managing to hold off the Justicars to prevent even more tension? Either that or the devs just didn't get to changing those things.

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I like your reasoning. Before Ulfric reared the entire ugly rebellion, the Thalmor might have left Skyrim Talos worshippers alone, rather than spend time and resources on Justiciars always patrolling Skyrim. +1 – ヴァイシャリ Mar 15 '12 at 17:46

You have a point about the temples. But if you talk to Heimskr he will say how he had to bribe some jailors to continue preaching about TALOS!

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Heimskr was actually supposed to be sent to jail if the Imperials win the battle, as per the Creation Kit. A bug prevents this, but the Unofficial Skyrim Patch (USKP) corrects this.

From the USKP v1.2.4 - (2012-11-21) version history:

When the Imperials get control of Whiterun during the Civil War, Heimskr will now be sent to jail as was intended.

UESP wiki, "Heimskr" article
USKP version history

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Could you cite an official source for this? A patch that's explicitly called "Unofficial" isn't exactly what one would immediately accept as primary canon. – Iszi Dec 1 '12 at 2:23
@Iszi The official source is the Creation Kit. There are a lot of game events that was actually programmed in the game, but bugs prevents those game events from happening (can be seen through the Creation Kit). The USKP aims to fix those. See the USKP version history. Search for the keyword 'intend' in the page for other examples like this. – galacticninja Dec 1 '12 at 5:27
@Iszi Another source is the UESP wiki article on Heimskr, which takes its sources from the Creation Kit. "Almost every Skyrim article on this site relies extensively on data taken from the CK." – galacticninja Dec 1 '12 at 5:34

The Thalmor are the ones outlawing Talos Worship. The Empire is more of a Talos worshiper than the Stormcloaks.

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Care to back up your statement regarding the Empire being "a Talos worshiper"? – kotekzot Nov 7 '12 at 2:05
The Empire was founded by Talos. – Shadur Jun 14 '14 at 10:16
@Shadur that didn't stop the Empire signing the White-Gold Concordat, which specifically prohibits the worship of Talos. – kotekzot Jun 14 '14 at 14:30
They were more or less forced to do so by the Thalmor by way of a treaty, and it's only really enforced when some Thalmor inquisitor is poking his nose in too thoroughly for them to let it slide -- and even then, killing a Thalmor inquisitor carries an informal fine on the level of littering as long as you don't leave his cronies alive to report it. – Shadur Jun 15 '14 at 14:21

talk to him, he has text explaining. side with imperials, ask about getting arrested "Oh yes, many times. But mighty Talos was my keeper, my shield against the heresy of the south! If not for Talos, and a few modest bribes paid to the right jailors, why, I would not be standing before you today, resplendent in my faith!"

not a bug, unofficial patch got it wrong, added something intentionally removed unless bethesda found it easier to add dialogue to gloss over it than make it work...

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