Arrow has probably not seen the last of Helix. Season 5 ended on a rather big cliffhanger. While Oliver was able to save his son William from Adrian Chase, it looked as though every other person in his life was trapped on Lian Yu when the island was ravaged by explosions. It won't be until season 6 that Oliver -- and the audience -- learns whether anyone was killed by Prometheus' final trap.
But that was not the only thread left dangling at the end of season 5. During the second half of the season, Felicity joined forces with hacktivist group Helix -- in spite of their questionable motives. Helix offered Felicity help several times, which she used to aid Team Arrow. In exchange they solicited Felicity's help in breaking their leader Cayden James out out A.R.G.U.S. imprisonment. Felicity expected Helix to continue helping her find Prometheus. However, the group left Felicity behind, not trusting her to remain on their side in the face of her crime fighting work with Team Arrow.
While Felicity was cautioned by pretty much everyone that Helix could not be trusted, it was only during their last appearance that she learned exactly how big a threat they are. And now that Cayden James is free, the danger is even greater. Co-showrunner Wendy Mericle recently spoke to TVLine about whether Helix will return in season 6:
"Having bailed on Felicity — immediately after using her to find and free their founder, superhacker Cayden James — Helix’s status is very much a dangling thread, and we don’t like to leave those hanging around. It’d be a great, sort of built-in story for Felicity to revisit these people, who are not very happy with her, let’s be honest. We left that open-ended on purpose, for sure.”
According to Lyla, Cayden James is incredibly dangerous. He was caught hacking an A.R.G.U.S. transponder and held without trial as a person of interest. Lyla even called him a security risk "20 times greater than Snowden." Now that he is free, and once more has all of Helix at his disposal, it is unknown what his next move is. The hackers in his group are at least as skilled as Felicity and Curtis, with much more information to work with. Odds are good that his imprisonment will give James a desire for revenge against A.R.G.U.S.
Mericle's answer does seem to imply that at the very least, Felicity will survive Lian Yu and return to Star City. Which is a good thing with Helix still on the loose. They are not a group that Oliver and the rest of the team can stop with weapons and punching. Felicity and Curtis are their best chance to fight fire with fire, and stop Helix from doing real harm in the future.
Arrow season 6 will premiere on The CW October 12.