A lot of ideas used in the Marvel's Agents of S.H.I.E.L.D. TV series originated in the comic book series Secret Warriors. The idea that S.H.I.E.L.D. was completely compromised by HYDRA and the remaining agents had to go underground. The idea that S.H.I.E.L.D. recruited a team a powered young people lead by Agent Daisy Johnson and her earthquake powers. Other than those underlying ideas the plot and characters of Secret Warriors bear no resemblance to the S.H.I.E.L.D. TV series. Don't pick it up expecting to see Agents Coulson or May. There is an Agent Eric Koenig, but he is in no way similar to Patton Oswalt.
What you do get with the series is a solid Bendis story about Nick Fury being an old hard-ass and bringing the Howling Commandos out of retirement to fight a global HYDRA conspiracy. You also get some intense comic book art by Stefano Caselli. Secret Warriors spun out of Marvel's Secret Invasion and Secret War events, but you don't have to know any of the context to enjoy the story on its own. Incidentally, Secret War (2004) should not be confused with the old Secret Wars (1984) or the recent Secret Wars (2015) both of which are unrelated stories from Marvel.