enigmatic puzzle - 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

Answer

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.