At the end of the quest but Emmie does not follow. She still sits after being told the coast is clear. Using free Pet Pal Mod and expanded followers mod. Tried dismissing extra followers and expanding party size to 8. Did not work.

Did you start the mod from an existing save in Fort Joy or was this a brand new playthrough?

I've got exactly the same issue. New game on definitive edition, no mods to tweak followers/party size.

Worth mentioning that I had the squirrel knight (the one that got added in definitive - rides an undead cat around), and the black cat (the one that follows you at the start in fort joy) already accompanying my party. Not sure if that might be affecting it? Even when the cat removed itself after escaping, Emmie still couldn't follow.

Whenever a save is loaded, Emmie will appear next to the party, but stay put and never move (unless combat kicks off, then her default aggressive behaviour kicks in). Can't complete the quest using this, as even when she's right next to buddy there's no dialog to resolve it.

Okay, thanks for the report and sorry to hear this, I have never seen it in my personal play throughs or from beta testers. I will try to reproduce it, but if anyone has a save game file that they could upload I would gladly make use of it so I could test with it. Was this single player or multiplayer run?

Mine is a Single Player Play Through. I also got dialogue from the Magisters when using the boat exit asking why the source hound was with me when Emmie was not physically there. I'd be happy to upload my save file but must confess some ignorance as these are literally my first Steam comments.

@acidproof - Oh, I did not necessarily mean to upload using Steam, just putting it anywhere like a Google drive. Not sure if it will work, but you could try this drive folder of mine and see if you can upload here:
https://drive.google.com/open?id=15fmXan4a4Z2v9oZlGmWpCtgzMR7Bcy5v

It appears I do not have permission to upload. I've started a new game and will give that a go. No worries, thanks for the help.

@acidproof @Janpu I have been trying to reproduce your problem, so far without success. I did seven test runs with different tactics, but Emmie always followed me when I told her to. Having the black cat and Sir Lora along doesn't seem to make a difference from what I can tell.

Could you please let me know what you did after accepting the quest from Buddy? Such as, did you leave Fort Joy and then come back inside to get her? Did you distract Bruno and the other hounds, or did you fight them? Anything else you can remember you did inbetween giving the blanket to Emmie and telling her to follow you? I'm really stumped by this issue...

I have asked Buddy who might know where the blanket might be, and he told me about the caves. In the caves I asked Frolie about it and she said Mody.
But since I've finished the Lord Withermoore quest already Mody is in grief and doesn't say anything other than begging Lord Withermoore to wake up. No dlalogue options.

Is there anything I can do at this point?

@Skaarphy - yeah if the Withermoore quest is finished in an unhappy manner then he doesn't want to talk. There are some minor clues if you walk around in the elf cave with Sir Lora or the black cat. That said, if Mody knows where the blanket might be perhaps you could look around a place Mody might frequent. ;-)

Right, got it. Thanks a lot! Now off to the happy ending. :)

Excellent, good luck and enjoy!

Restarting the campaign resolved things for me. I was able to progress normally and Emmie followed me this time. Not sure what happened before but thanks for looking into it.

@acidproof - Glad to hear that, thanks for the feedback! Enjoy the happy reunion :-)

Hello have the same problem as above here is a save file your link did not let me up load
https://drive.google.com/open?id=18lf7j5eNTqHiuYpAAT7x2Jya2EwHIHaE