However, executive producer Stephen Nathan has now confirmed to TV Line that four extra Bones episodes have been ordered, though it is currently unclear when they will air.
"It's a very odd situation we're in," he said. "[Fox] has scheduled us for 13 episodes, but they want as many episodes as we can produce."
He continued: "We're constructing the season so that the finale is episode 13, and then there will ultimately be four more episodes that we can play with. [Fox] could run them on a different night, they could run them in the summer, or they could hold them for fall ."
Nathan added that the four new episodes will be standalone and could function as a "mini-season".
"Because the show is centrally episodic, and we know what's happening with Booth (David Boreanaz) and Brennan, we can do four great episodes that are almost like a mini-season," he said.
"We can do a four-episode mini season after the 13-episode regular season. It's weird, and it's a challenge, but we'll do it."
Bones returns to Fox on Thursday, November 3 at 9/8c.