Avengers: Age Of Ultron Ending - 14 Implications For Phase 3 And Beyond
6. Thanos' HYDRA Links
At some point, Marvel is going to have to explore how and why Thanos was linked to HYDRA and how far the rabbit hole goes, because the mid-credits sequence all but confirmed some collaboration.
In accepting that he now has to "do it himself", Thanos is now resolved that his allies have all failed him. The suggestion from Age Of Ultron was that HYDRA were somehow in cahoots with the big purple alien, but if that was the case, why didn't he simply take the Infinity Stone for himself, rather than allowing them to experiment with it to make Enhanceds.
If Marvel are smart, they will turn what amounts to a confusing plot-hole into a story detail that somehow closes the loop between the two villainous factions. Perhaps that answer will come with Baron Zemo? Perhaps it never will.