The Shadow Council refers to both the C Team fandom and an actual organization within the C Team universe. C Team episodes often begin with DM Jerry Holkins telling the audience, "Shadow Council, may our labors please you". Elyssa Grant, the show's producer who also works closely with the fans, is known as the 'Shadow Chancellor'.
Animated recaps of the season arcs made by Zee Bashew and written by Jerry are narrated by a living skull named Mimir, who bears the barbed 'S' symbol that represents the Council and refers to himself as their 'humble servant'. Mimir also begins his narrations with "revered Shadow Council, may my labors please you", and then proceeds to describe the C Team's latest adventures as if giving a covert report on the "franchise of your interest". He uses phrases such as "your supposition was correct" to give the impression that the Council is actively paying attention to and involved in the C Team's activities, also referring to their gifts to them.
Jerry and Elyssa have allowed the audience to influence certain directions in which the game is run, offering them polls asking which of several choices they want to see happen in the game. The audience on the Twitch stream can also donate bits to the show, directing them towards particular players, who then accumulate charges that can be spent on an ultimate ability or on rerolling dice. The cumulative total of donated bits is also added into a 'DM's Cauldron', which when full, results in Jerry causing a momentous event to happen in the game. Recently, the game Idle Champions of the Forgotten Realms has created 'Omin's Challenges' which also go towards filling the cauldron and can influence the direction of the event.
For merchandising purposes, the symbol of the Council was later changed to a triangle displaying three hooded skeletons around an all-seeing eye.
True Nature of the Shadow Council (spoilers for seasons 1 and 2)
Rosie Beestinger revealed that she has a past that involves Asmodeus, the devil lord of the Nine Hells and a god in his own right. She used her prior connections with him to help cement a deal that saved Strix from destroying the multiverse, but hinted that this came with repercussions.[7,8] After Asmodeus appeared at Brahma and Walnut's wedding and helped them stop an invasion of monsters sent by the Sanguilith, he tried to persuade other members of the C Team to sign contracts with him, and Rosie was quick to sit them down and warn them with her own story--about how when she was young she made a deal with people linked to Asmodeus to gain power, money and popularity; a bargain she now regretted.[9,10] This fits with her background of being the mob boss 'Grandmother Night', and why many of her adopted Beestinger children were in fact the orphans of prior hits, and why some of them want to kill her. Earlier, she had revealed that the group she had bargained with was in fact the Shadow Council, and that they had sent her missives before, but that the source of those orders is "obscure" and "a power I would not be able to negotiate with anyway", with Kate then outright naming Asmodeus himself. It is unclear if the Shadow Council might also have a connection with the monastery of the Way of the Shadow that trained Rosie as a monk, but Kate had said that she does still have unfinished business with them that she wants to bring up in the game.
Rosie explained that the kill markers--black rectangles with the barbed S at the top and the name of the person she was to kill on the other side--only came to her every 15 to 20 years. She had not received one since joining the C Team, until one arrived with Omin's own name, something that angered Rosie as she felt it was a form of manipulation. She explained that there would be serious consequences not only to herself if she did not follow through, but to everyone close to her, including the rest of the C Team. When Walnut revealed this to Omin, he claimed he had always known about Rosie's background and that it was one of the reasons he had hired her, but he was surprised to find himself her next target. He later explained to Rosie that he owed the Council a lot of money for help finding his sister Auspicia. He also elaborated that although the Shadow Council themselves weren't concerned with things like money, there was "an organization that surrounds them that collects on their debts" and "operates on a different moral wavelength", called the Umbra (represented in Kris's animation as a broken off piece of the triangle emblem). Omin asked Rosie if she could try to get in touch with them for him, but she was unable to find them until she herself was approached by one of their secret members, who was disappointed that Rosie had not yet done the deed. When Omin was later pulled into hell and told by a pit fiend that he had been "delivered to us; this is where you will remain", Omin managed to trade it Jim Darkmagic's clone's soul instead.
 AMA with CTeam Producer Elyssa & DM Jerry! C Team Reddit.
 C Team Animated Recaps page. Penny Arcade website.
 Here's the link to the official Shadow Council logo art, straight from Elyssa. C Team Reddit.
 Waffles Inc, Part 5.
 Idle Champions of the Forgotten Realms Interview, 3/21/19. Twitch.com.
 C Team S2E25, Promise, Part 14 (2:30:55-2:31:54) and S2E26, Matriarch, Part 1
 C Team S2E35, Matriarch, Part 9 (-)(1:59:00-2:01:22)
 C Team S2E25 Table Talk (12:40-13:07)
 C Team S2E29, Matriarch, Part 3 (18:50-26:05)
 Acq Inc: The “C” Team: Matriarch (abridged). YouTube.
 Acquisitions Incorporated, PAX West 2018 (1:59:20-2:07:45) (2:20:20-2:26:00)