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.
