This is the Artificial Intelligence issue - Two stories: one about the Ark and the A.I. that controls it, the other about Friday growing up as a teenage A.I.
The first story tells about how that S.H.I.E.L.D. has a literal Ark on Mount Ararat (where perhaps the Biblical Ark of Noah rested after the flood). This Ark has scientists and DNA material that could start a second Earth if this Earth ever becomes globally threatened with extinction. This A.I. threatens all of humanity by turning on its creators and launching the Ark as it determines the humans have threatened their own Earth, and it begins the Earth 2.0 protocols. Tony Stark as Director of SHIELD comes to stop the A.I. and stop the launch of the missile with all it's resources including the scientists.
The second story is of Friday, Tony's personal A.I. who is acting like a selfish teenage girl and kidnaps Pepper. Pepper realizes that the A.I. just has a crush on Tony, and Tony instead of destroying or disabling Friday, puts her in a time-out and then begins to spend more time with it to help guide her more as a parenting influence.
