Agents of S.H.I.E.L.D. could be setting up the Framework as a returning enemy for season 7. When Agents of S.H.I.E.L.D. launched in 2013, it was essentially the MCU's official tie-in TV series. Over the years, though, the show has developed a mythology all of its own, one that incorporates everything from Inhumans to time travel, from alien Confederacies to an all-new Ghost Rider.
One of the most fascinating ideas was the Framework, a virtual reality created by Professor Radcliffe in Agents of S.H.I.E.L.D. season 4. Radcliffe's goal was to establish a virtual reality where death had been conquered, and to upload minds into it, where they could live forever in a Utopian world. It went badly wrong, with conflicting desires and a, frankly, insane artificial intelligence instead creating a twisted reality where the world had been conquered by Hydra. In the end, the Framework was apparently destroyed.
Agents of S.H.I.E.L.D. season 6 has confirmed that the Framework isn't truly gone after all. Radcliffe created the Framework by scattering fragments of coding across every computer system in the world, and fragments of that coding survived - enough to actually reconstruct complex, sophisticated virtual environments. Deke Shaw, the time traveling grandson of Fitz and Simmons from an alternate future, has founded a tech company dedicated to exploiting Framework code. He's using it to create virtual reality action games inspired by his future timeline and experiences with S.H.I.E.L.D., and couldn't resist adding a highly objectified version of Quake.
On the face of it, this all seems pretty innocent - even if Daisy is less likely to agree if she ever learns of her Framework NPC. In reality, though, Deke is playing with some dangerous technology. It's important to remember that Radcliffe created the Framework after reading the Darkhold, an ancient tome filled with forbidden knowledge. In the comics, the Darkhold is a corruptive force, fashioned by the Elder God Chthon, who's one of Marvel's Satan-equivalents. Deke is playing with forces he cannot possibly understand.
Furthermore, it's reasonable to assume Deke won't be the only one to discover this coding. While Deke certainly has something of a head start, given he'd stumbled upon Framework tech in his own future timeline as well, the reality is that these fragments of Framework coding are probably in every computer system across the planet. There's no doubt that other computer scientists will be looking at this rogue code, trying to figure out what it is, how it got into their systems, and what they can do with it. The Framework genie is well and truly out of the bottle. Deke's goals may be innocent, but others could come up with far more dangerous ideas for this dark technology. Those could include anything from sophisticated brainwashing to enhanced interrogation, and making matters worse, it's actually possible for beings to transition from the Framework into the real world. A Framework reality could potentially invade Earth.
Of course, there's no way this kind of plot is going to be woven into Agents of S.H.I.E.L.D. season 6; this season is focused on a mission to space, as well as the mystery of the new Coulson. But season 7 is already in the works - and the threat of the Framework could well be a major part of it.