Farewell Emrakul, here's a truly puzzling goodbye

Sadly, our moderator Emrakul is stepping down. They've done a fantastic job, so if they have to leave, let's see them off in true puzzling fashion!

There is a message for them hidden here, can you find it?

Allocate (6)
Possessed (3) Oak fruit (5)
Behind (3) Charged Particle (3)
Arm End (4) Thick paper (4)
Washing bowls (6)
Jewish skull cap (8)
Create (4) Draw parallel lines (4)
Help (3) is departed (4)
Japanese car company (6)
Child’s object (3) female domestic servant (4)
Makes a difficult to remove mark (6)
Curved structure (4) Arm’s end (4)
Very old (4) charged particle (3)
Canine (3) IX (4)
Infant (3) is departed (4)
Firm (4) cylindrical containers (4)

What is the message?

Hint:

The promised end

Second hint:

Character names are the key to a story

• This is relevant to Emrak's name. The first step can be done, the second requires some extra knowledge – Beastly Gerbil Apr 28 '17 at 6:15
• … first requires knowledge or that is already Steganography? – Jan Ivan Apr 28 '17 at 6:58
• @JanIvan No, the first step isn't really anything, the second step requires knowledge to do steganography – Beastly Gerbil Apr 28 '17 at 7:02
• I mean: Oak fruit (5) => Acorn, or Jewish skull cap (8) => yarmulke, that is knowledge imo. But if I'm going wrong way..... because Arm’s end (4) or Arm end (4) I have no idea, so that's why I'm asking. – Jan Ivan Apr 28 '17 at 7:08
• @JanIvan that's correct, and that's not the knowledge – Beastly Gerbil Apr 28 '17 at 7:24

The message is

GOODBYE AND THANKS.

Here are the solutions to the clues:

 G ASSIGN Allocate (6) O HAD ACORN Possessed (3) Oak fruit (5) O ASS ION Behind (3) Charged Particle (3) D HAND CARD Arm End (4) Thick paper (4) B BASINS Washing bowls (6) Y YARMULKE Jewish skull cap (8) E MAKE RULE Create (4) Draw parallel lines (4) A AID GONE Help (3) is departed (4) N NISSAN Japanese car company (6) (D)TOY MAID Child’s object (3) female domestic servant (4) T STAINS Makes a difficult to remove mark (6) H ARCH HAND Curved structure (4) Arm’s end (4) A AGED ION Very old (4) charged particle (3) N DOG NINE Canine (3) IX (4) K KID GONE Infant (3) is departed (4) S HARD CANS Firm (4) cylindrical containers (4)

Observe that

solutions fall into groups that are near-anagrams. The columns at the left hold the discrepant letters. They spell out GOODBYE AND THANKS. I will explain the wrong-looking TOY MAID line below.

Now, the

"non-discrepant" letters in each set are: ASSIN, HADACRN, ARMULKE, IDGONE. These are anagrams of NISSA, CHANDRA, EMRAKUL (of course!) and GIDEON. The only one of these I found was EMRAKUL; elias, in comments, found the others and remarks that they are important characters associated with Emrakul in Magic: the Gathering as described e.g. here. And now (again, this is elias's find) we can explain TOY MAID too: it's D plus TAMIYO, another such character.

So in fact

I think my formulation above in terms of near-anagrams is misleading; the actual rule is that each row yields an anagram of an MtG character associated with Emrakul, plus one other letter.

• Oh very nice find - I think this is most if not all of it – n_plum Apr 28 '17 at 15:48
• There are two 8-letter sets, no? EMRAKUL and HANDCAR. Not that I have found a better anagram by adding it. – M Oehm Apr 28 '17 at 16:12
• Looks like these are anagrams of Gideon, Nissa and Chandra, who are all important characters in this story - also Tamiyo appears, which explains 'TOY MAID' – elias Apr 28 '17 at 16:30
• @elias: Aha, hence the knowledge tag. – M Oehm Apr 28 '17 at 16:32
• Aha! That would be knowledge I completely 100% didn't have. Thanks, @elias! Will update answer accordingly. – Gareth McCaughan Apr 28 '17 at 17:09