Cisco's responsible for what went wrong in the stinger, you know. Julian told him to grab the oxygen. But instead, Cisco was using an Ambu bag (trademarked name), generically known as a bag-valve mask or a manual resuscitator, which only provides what oxygen is in the atmosphere. Of course, Julian shares in the responsibility, as he didn't correct Cisco's mistake.
And I'm not sure that I trust H.R.'s explanation for his two-day absence, given that Caitlin started going south after he showed up. Preliminarily, I'm thinking nanites, passed to her when he reached for the gelatin (semi-serious guess).