The answer to who stole Superman’s body is revealed in Action Comics #686.
Action Comics #686
Triangle Number 1993 – 8
Writer: Roger Stern
Penciler: Jackson Guice
Inker: Denis Rodier
Colorist: Glenn Whitmore
Letterer: Bill Oakley
Much like Adventures of Superman, this entire issue was omitted from the 2007 Omnibus. I know I’ve discussed that edition and its shortcomings quite a bit, so let me take a moment to discuss the other two printings. In 2013, DC redid the omnibus outright. They commissioned a new cover by Jurgens and Ordway and did indeed restore the things that had been omitted from the previous edition. The back matter stayed the same, but the paper stock was changed from newsprint to glossier modern page stock. In 2016, alongside the new complete trade paperback collection (broken into five books: Death of Superman, Funeral for a Friend, Reign of the Supermen, Return of Superman, and Doomsday — the last covering later appearances by the monster) they reprinted the omnibus with an all-black cover. The only other difference between the two latter editions is that the newest one also includes the 1993 Superman Annuals. Both are also larger in size than the original, not just in length.
The issue opens with a scene of Guardian stopping some carjackers. Much like the Gangbuster sequence from the Adventures issue, this sets the tone that Metropolis has become a much more dangerous city in Superman’s absence. It’s a way to make that loss feel a little more real. After he deals with the crooks, he’s summoned back to Cadmus urgently by Dubbilex.
In an aside with Lex Luthor, we are given insight into his current schemes, in that he’s paranoid that the entire situation is a ruse by Superman to catch him off guard. After all, he faked his death, so why couldn’t Superman do the same. This is a typical trap that narcissists tend to fall into, where they believe that everyone else must be accountable for the same crimes they are.
In a parallel both Lex Luthor and Director Westfield twist truths and language around to explain their actions when questioned. When Luthor is asked why there are secret access tunnels into the tomb, he claims it was originally intended to be a time capsule and was only converted to a tomb to fill the current need. Likewise, when Westfield is confronted by Guardian about Superman’s body, Westfield says that the President only told him to let Metropolis have its funeral first. This is where the plot to clone Superman and return him to life is established, but the geneticists are having trouble getting a sample because even in death Superman’s skin is invulnerable.
While continuing to hunt for the body of Superman in the tunnels below the tomb, the S.C.U, Supergirl, and Luthor come across an explosive charge with the Cadmus logo on it. The charge goes off opening a hole to the river above, flooding the tunnels, and almost killing the search party. For now… Cadmus is safe.
The last scene of the issue is Lois bidding adieu to the Kents and Lana. She and Lana share an emotional embrace and tears over the loss of the man they loved.