The Mary-Sue mothership takes on the same concept of Mary-Sue (or Gary-Stu, depending on the case), but this term stands for both the Mary-Sue and the Suethor who created the Mary-Sue in question.
In this case, however, the 'pairing' between the Mary-Sue and the canon character will have gathered a club of fans who follow the Suethor's every art or literature featuring the Mary-Sue and canon character, of whom would, 99.9% of the time, be turned OOC (out of character).
The Suethor's avid fan club becomes very loyal to the Suethor, giving the Suethor art gifts featuring the Mary-Sue in scenes with the canon character in their own artistic style.
Mary-Sue motherships are more than likely to be found at DeviantART, but some Suethors show off the work of their followers at Photobucket or other image site.
If there is ever a setting where a Gary-Stu character is involved, it is termed the "Gary-Stu Death Star."
The numerous images featuring the Mary-Sue and canon character fighting against the world or having babies can be termed "Mary-Sue motherload."
"Holy crap, I just spotted another Mary-Sue mothership. M-S MOTHERSHIP! TWELVE O'CLOCK!! IT'S HEADED RIGHT FOR US!!"
At the very heart of a Mary-Sue mothership is an insecure individual who is angsty and only wants to elope with a towdally osm fictional character who will marry them, give them babies, and live happily ever after. The End.