Warning: SPOILERS for The Man of Steel #5
One of the mysteries of Brian Michael Bendis' The Man of Steel has been solved and it concerns Superman's father, Jor-El. One of the previous big twists of the DC Rebirth era is that Jor-El didn't die with Krypton. Instead Jor-El was saved to become the new (sort of) villain, Mr. Oz.
When Superman first encountered Jor-El (and Oz) the story seemed to come to a final conclusion. Jor-El, at first, seemed militantly opposed to his son's life as Superman, believing that humanity wasn't worthy of Clark Kent's powers. Eventually though it was revealed that Jor-El was under the control of some much more powerful force, presumably Dr. Manhattan, and that he greatly regretted his actions. However, Jor-El was violently taken by some portal before Superman could really help his father. The Man of Steel #5 seems to have thrown all of that development out the window.
The Man of Steel #5 isn't Jor-El's first appearance in Bendis' run on Superman. The character previously appeared in the previous issue as the mysterious figure whose been haunting Superman's flashbacks of his missing family. The Man of Steel #5, however, makes Jor-El's intentions very clear and it's all to do with his grandson, Jon Kent A.K.A. Superboy.
This isn't exactly a new goal for Jor-El to have either. In his first (re)appearance during Dan Jurgens' run on the Big Blue Boy Scout, Jon did become a bit of a pawn in the battle between his father and grandfather. Jor-El believed that Jon could become the Superman that Clark didn't because Jon was young and not too tied down by his affection for humanity. Clark, meanwhile, realizing his supposedly deceased dad was crazier than a bag of cats in heat wanted Jor-El nowhere near his kid.
In The Man of Steel #5 nothing has changed. The scene, which takes place some weeks before the current timeline of the story, is all about Jor-El demanding Jon go with him in a tour of the universe. Jor-El talks directly to Jon, because in Kryptonian culture he's old enough to make his own decisions, and Jon, because he's a typical stupid American boy, agrees to go with his grandfather. Unsurprisingly Clark and Lois Lane have a huge problem with this arrangement.
Jon won't be moved though and neither will Jor-El, especially after the latter claims that the trip around the galaxy will only be temporary. Lois eventually acquiesces on the condition that she accompany Jon because she won't let her son go on a space trip with a total stranger. This explains why, in the "present day," Lois seems to have left Clark and run away with their son. It's technically true but Superman and Lois' marriage isn't in any real danger. However, the lives of Jon and Lois definitely might be in jeopardy.
The Man of Steel #5 is certainly occurring after the events of Action Comics #987 to #992 when Jor-El was first unveiled as Mr. Oz. This is clear not only in the way that Clark and Jor-El are speaking to one another but by Jor-El's appearance. Jor-El isn't holding his staff,. It was implied in the very last issues of Jor-El's original arc that the staff was, somehow, controlling his actions and that Jor-El wasn't as bitter or as violent as he seemed. The absence of the staff implies that Jor-El is in his right mind and he still believes Jon to be the powerful heir that Superman can never become for him.
Of course The Man of Steel #5 is still a Brian Michael Bendis story. The writer is famous for introducing one seemingly game-changing twist and swapping it for another at the last second. Jor-El definitely appears like he wants to take Jon Kent and mold him into the perfect and violent Superman Jor-El believes that broken Earth needs. Jor-El's goals, however, could be much more altruistic.
Superman is currently fighting a new villain Rogol Zaar. Part of Zaar's plan is to exterminate all Kryptonians left in the universe (for reasons still to be unveiled). In his past, Zaar had some kind of connection with Jor-El,So it's possible that Jor-El knew Zaar was coming and is merely acting like megalomaniac to take Jon (and Lois) away to safety. Jor-El doesn't truly want to replace Superman with his son but merely protect the family he has left. This twist wouldn't match Jor-El actions in the issue but would make sense in his overall arc.
The Man of Steel #5 is available now from DC Comics.