You have to take the eye-gem to the baths with you. Burry should offer it to you when you get ready to leave the tavern. After that, just keep following Rune’s route and you should get it. Key difference that happens is when Rune uses the eye-gem (putting it in his closed eye), and his sprite will show a golden yellow eye on one side!
Viewing post in Shelter (Furry Visual Novel) comments
No, you should be able to skip as long as you haven’t seen the scene already. I went through tested different choices, and as long as Rune has the gem after his Training session and throws it at you, you catch it, and Alon is there at the baths, you should get the scene. I also tested to see if it was because of who you choose to save, and that has no effect on the outcome of the scene, just the Ending scene right before the credits.