The differences in LN1-3 are relatively minor. While there are quite a lot of minor changes and tidy-ups, it’s largely the same. Most of the changes are in the side-chapters (non-Kumoko chapters), including quite a few entirely new scenes and chapters. LN3 ends with Kumoko exiting the Labyrinth for the first time.

One bigger change is the introduction of a new character, effectively - while Shun has a dragon in the WN, it only has a minor presence. In the LN, this dragon is actually a reincarnator. We see the egg in the manga (which is based on the LN), and that egg is eventually given to Shun and hatches (initially looking like a lizard) sometime after Shun has the public unveiling of his status. It’s a while before either of them realise that they’re both reincarnators.

This dragon is girl called 漆原美麗 - Shinohara Mirei. Her name doesn't come up in the WN at all but she's there from S1 in the novels when we see the classroom from Shun's POV. Oka-chan caught her using a mobile phone while in class. Also, she was one of the girls bullying Wakaba Hiiro: Mirei confessed to a senior but got rejected because he was in love with Wakaba, so Mirei took her frustrations out on Wakaba. She would have been the prettiest girl in class if not for Wakaba and she has quite an outgoing personality. She was disappointed to find out that her “prince” was Shun.

In LN2, with some help from the others she is able to level up a lot and becomes much bigger. In LN3 she becomes a Light Earth Drake due to Shun becoming the Hero. She’s called Feyrune, or Fey for short. She seems quite accepting of herself being a dragon but would like to become human if possible.

There’s an extra chapter from Julius’s POV where he and his entire hero party are battling with a single one of the “babies” (aka Remnants of the Nightmare) and they’re having a hard time. They might not even have won if it hadn’t have been distracted by something.

At the end of LN2 is brief chapter that simply contains D’s thoughts, which I’ve translated below:

Her actions seem to indicate that she is pleased with Wisdom. Even if saying so for myself, it was indeed worthwhile giving it to her as a present. Showing such an extreme response - she was happy with it for sure. I will make certain to permanently preserve the images of her setting her bottom on fire and going into a panic. I am sure that if it is Kumo, she will surely be able to master Wisdom as well. After all, even when dividing her consciousness, she completely took it in her stride. Since she already holds two Ruler skills, Pride and Patience, I am sure that she will be able to manage even if she gains another one. Also, please reach my existence someday, okay. I will be waiting for you. I am sure that you in particular will be able to entertain me. Even me who is an Administrator and Evil God. Now then, what will you show me next, I wonder? How will you involve yourself with this world after this, I wonder? How will you change this world after this, I wonder? I am very much looking forwards to it.
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In the Human-Demon Great War, quite a few of the details are skipped over and we don’t see Shiro fainting due to her delicious food being eaten by others. Also, Shun never sees what happened through a memory crystal - it is simply described to him.

After Kumoko kills Alaba, there’s an extra chapter from Ariel’s POV (in the future timeline) talking about her having killed dragons in the past. It’s from Balto’s POV. It gives the impression (to LN only readers) that Ariel is future Kumoko.

The biggest change in LN3 is the early appearance of Sophia - her first appearance is when Sue shoots her father while brainwashed and Shun is captured by Yuugo. In the WN, Shiro had simply told Sophia to kill the Potimas clone but here she was probably told to protect Yuugo just in case. In the LN version of the scene, Shun is able to briefly break free but Sophia appears to protect Yuugo. Shun thinks she looks like a princess straight out from a fairy tale book in looks but she has an incredibly sinister aura (he’s basically scared of her right from the start, having good intuition). Sophia is really relaxed about everything, having time to tease, and also neutralises all magical attacks made against her. When Oka-chan turns up to rescue Shun, she immediately recognises Sophia and panics. Sophia lets them get away though.

Later, when Shun is trying to escape the castle grounds, Sophia turns up again, tossing in Potimas’s head (obviously she killed the clone anyway), shocking Oka-chan. It’s also now clear that Sophia is a reincarnator, but not who at this point. It’s not known how Oka-chan and Sophia know each other. Sophia’s also provoking them a lot and it turns into a fight. There’s some ninja-like people with Sophia too (Felmina and Waldo). Sophia knocks out Oka-chan but Fey turns up to save the day, carrying off Shun. Following that is a brief scene between Sophia and Felmina with them both being quite tsun-tsun to each other, and it’s also clear that Sophia let Shun get away, and Felmina goes off to report to “goshujin-sama” about Sophia’s actions (she wasn’t supposed to fight Oka-chan), to Sophia’s distress.

Later when Shun raids the capital (to save his brother etc), after the brief fight with Ronant there’s a scene between Ronant and Sophia from Ronant’s POV. Sophia is being provocative again (she’s a battle maniac after all) but let’s Ronant off (she knows he held back against Shun). He’s quite nervous about the whole encounter since he can tell she’s much stronger than him and is even more nervous about her “goshujin-sama”.

At the end of LN3, Kumoko has finally exited the labyrinth (though she’s not Zana Horowo yet, unlike in the WN).