"They're coming". Blackshirt's mixed expression of anger and fear in reaction to Jacob's last words suggests whomever "they" are, their arrival is both unexpected and a respectable threat to him. This may not tell us who "they" are, but it tells us who "they" aren't.
"They" couldn't be Ilana and company. Blackshirt already knew of Ilana and her crew from flight 316. He went so far as to address their "threat" directly with Richard: "Once I've done that ['thanked' Jacob], we're going to need to deal with the rest of the passengers from the Ajira flight that brought me here." (The Incident, Part 1) He is fully aware of them and is preparing Richard for their elimination.
"They" couldn't be the '77 Losties (Jack and company) either. If you believe that Jacob and Blackshirt are engaged in an epic game, and that the people who are brought to the island are the pieces, it makes no sense for Blackshirt to be mortified that they would be "coming". They are only the pawns - since when was a gameplayer afraid of a piece of plastic? Besides that, Jack, Kate, Hurley, and Sun were among the passengers from the Ajira flight; I believe Blackshirt means them as well when he instructs Richard to deal with the Ajira flight passengers. If the '77 Losties are destined to return to this time of Blackshirt's triumph over Jacob, Blackshirt is fully aware of them and planning for them.
So who are "they"? It wouldn't be the first time the Lost writers introduced a new group of characters to the stage while misdirecting the audience. Having set the expection of "The Others'" existence throughout Season 1, a group that Jin calls "Others! Others!" appears, capturing Jin, Michael, and Sawyer (Season 2, Adrift, Orientation). We soon learn that these aren't "The Others" that Danielle warns of, but the 815 tail passengers (Ana Lucia, Eko). That misdirection opened up an entire new branch of storytelling.
Jacob's and Blackshirt's relationship as defined in the opening scene of The Incident also opens up a new branch to this story, and it would make sense if new characters came with it. I expect that we haven't seen this "they" yet, and that their introduction will come in season 6. Judging by Blackshirt's reaction to Jacob's warning, this new group is more likely to be Jacob/Blackshirt peers rather than pawns.
"They" couldn't be Ilana and company. Blackshirt already knew of Ilana and her crew from flight 316. He went so far as to address their "threat" directly with Richard: "Once I've done that ['thanked' Jacob], we're going to need to deal with the rest of the passengers from the Ajira flight that brought me here." (The Incident, Part 1) He is fully aware of them and is preparing Richard for their elimination.
"They" couldn't be the '77 Losties (Jack and company) either. If you believe that Jacob and Blackshirt are engaged in an epic game, and that the people who are brought to the island are the pieces, it makes no sense for Blackshirt to be mortified that they would be "coming". They are only the pawns - since when was a gameplayer afraid of a piece of plastic? Besides that, Jack, Kate, Hurley, and Sun were among the passengers from the Ajira flight; I believe Blackshirt means them as well when he instructs Richard to deal with the Ajira flight passengers. If the '77 Losties are destined to return to this time of Blackshirt's triumph over Jacob, Blackshirt is fully aware of them and planning for them.
So who are "they"? It wouldn't be the first time the Lost writers introduced a new group of characters to the stage while misdirecting the audience. Having set the expection of "The Others'" existence throughout Season 1, a group that Jin calls "Others! Others!" appears, capturing Jin, Michael, and Sawyer (Season 2, Adrift, Orientation). We soon learn that these aren't "The Others" that Danielle warns of, but the 815 tail passengers (Ana Lucia, Eko). That misdirection opened up an entire new branch of storytelling.
Jacob's and Blackshirt's relationship as defined in the opening scene of The Incident also opens up a new branch to this story, and it would make sense if new characters came with it. I expect that we haven't seen this "they" yet, and that their introduction will come in season 6. Judging by Blackshirt's reaction to Jacob's warning, this new group is more likely to be Jacob/Blackshirt peers rather than pawns.