“Purpose in the Machine” is episode two of season three of Marvel’s Agents of S.H.I.E.L.D.
Although everyone else believed that Simmons was dead, Fitz did not, and at the end of the previous episode, “Laws of Nature”, he was revealed to be correct, as she was alive, just not on Earth.
This episode opens in Gloucestershire in England in 1839 with a group of men investigating the Monolith themselves – largely by sending people through it – before returning to the present. Fitz has managed to discover sand on the Monolith, and there’s no way it could have got on it. The theory is that it is possibly a portal. To investigate further, they recruit the Asgardian Professor Elliot Randolph, last seen in “The Well”, to help.
Hunter is going after Ward by himself, and Ward is trying to rebuild HYDRA. May is staying with her father and considers herself to have left S.H.I.E.L.D. – permanently. Skye – “it’s Daisy” – is trying to get May’s ex to speed up the process of recruiting new Inhumans for her team, as he so far hasn’t approved a single one.
Not only are S.H.I.E.L.D. and a new government agency, the ATCU (who seem to be more interested in killing them) hunting down the new Inhumans, there’s another party. So far, this just seems to be a big, powerful, sort-of alien looking creature.