WARNING: This article contains major spoilers for Man of Steel #4 by Brian Michael Bendis, Kevin Maguire, Jason Fabok, and Alex Sinclair, in stores now.
Man of Steel has pitted Superman against the out of control, genocidal alien powerhouse Rogol Zaar as he seeks to wipe out the last remaining Kryptonians in the universe. He is getting close to fulfilling his goal after destroying the city of Kandor and taking the fight to both Superman and Supergirl in the streets of Metropolis. However, in Man of Steel #4, Rogol Zaar turns his attention to a new target: Jonathan Kent.
Following their epic battle, Superman and the alien warlord meet in the ruins of the Fortress of Solitude, and Rogol Zaar asks him if he has any children. If this villain is to truly "cleanse" the cosmos of Krypton, his attention will have to eventually turn to the child Superboy, but it appears someone has decided to intercede. Earlier in the issue, we see this persons finally step out of the shadows to reveal they're none other than Jor-El, Superman's father, and he's come to take his grandson, presumably to safety.
A Father Returns for the Son
The main feature in Man of Steel may focus on Superman's conflict with this new villain, with the bulk of each issue drawn by a different artist, but a second story has been unfolding at the same time. Each issue contains a two-page sequence drawn by Jason Fabok regarding the arrival of a mysterious presence. Lois Lane and Superboy are secretly missing, but what exactly happened to them has been slowly unfolding over the last few weeks. In the fourth issue of the series, it is revealed that Jor-El paid the Kents a visit, and he is hoping to take possession of Jon.
The Kryptonian grandfather has, of course, recently shown up in various Superman stories. During Dan Jurgen's run on Action Comics it was revealed that Jor-El had been plucked from time at the exact moment of Krypton's destruction. Doctor Manhattan is believe to have spared him and sent him to Earth for some as-yet unraveled reason, where he experienced the very worst humanity had to offer before ultimately determining that Superman must abandon the human race. Jor-El was mysteriously pulled away again and has not been seen since.
His reemergence just as Rogol Zaar is coming for the last remaining Kryptonians should not be considered a coincidence. The alien warlord revealed that he knew Jor-El well before the planet's destruction. If Superman's father is back, here and now, it is because he knows what his son is up against, and he is here to help. As misguided as Jor-El previously was, he always meant to do what was in the best interest of his grandson.
What we might soon learn is that Jor-El came to his son in order to keep his family safe from harm before Rogol Zaar had a chance to hurt them. It has been hinted that Lois and Jon have not been seen in public for quite some time, and people are getting curious. Kal-El—as both Superman and Clark Kent—seems to have no knowledge of their location, though memories continue to flood back from time to time. It's why that part of the plot has been so slow to be revealed: Superman doesn't remember. It is possible that Jor-El hid them from danger, and also made sure that Superman knows nothing about their location.