I have a very messed up theory that Rising Tide is actually Ultron. For some reason, I feel it is somehow related to him and his machinations for Avengers: Age of Ultron. I mean it would be a nice set up and I'm only fan guessing but it reminds me alot of The Master in S3 of Doctor Who if they go by my theory. Ultron may have been created way before The Battle of New York as a meager AI by WSC (World Security Council) and SHIELD's darker folk and then may have been projected by them to be built after the Extremis incident to rely on his ability to think up of counter measures for threats alien and terrestrial. While he is being built, he manipulates organizations from all over the world from behind the scenes through many of them including the Rising Tide as a meager AI to get them to depend on him unwittingly, thus making his importance all the more needed for the benefit of humanity. If I suspect what Winter Soldier is to go by, Ultron may also have a hand in the events of that film that may suspect he is an AI controlling everyone until his body is built for the 2015 showdown using Stark tech while Agents of SHIELD may have to deal with Skye's association with the genocidal robot. Once Age of Ultron arrives, he realizes humanity's flaws are extremely vast and will somehow pin this through the avengers themselves, setting his rage and desire to replace humanity with his own image. I may also theorize that Skye's Rising Tide may end by the time the movie comes out as well.