In light of Jonathan Kent's future as the next Superman, now seems as good a time as any to examine his past. The current Superboy has two separate origins, one in which he was born to the pre-Flashpoint Superman and Lois Lane and one in which he was born into the current DCU under much more normal circumstances. But in his very first origin story, Jon Kent was delivered by his father while the Batman of the Flashpoint universe, Thomas Wayne, provided assistance. This would become a trend in Jon's next birth with Batman and Wonder Woman standing guard while Superman and Lois focused on the most important day of their lives.
In Convergence: Superman #2 by Dan Jurgens, Norm Rapmund, and Tom Napolitano, multiple cities from across the multiverse were kidnapped by a being named Telos to battle each other for survival. The pre-Flashpoint world was pitted against the Flashpoint universe in an ironic twist.
The Flashpoint version of Superman, known to his fellow heroes as Subject One, had a different goal. This version of Kal-El was isolated all of his life, but developed a connection to Lois Lane as she was the only one who treated him with kindness. She was tragically killed however, traumatizing him. So when he heard that an alternate Lois Lane was alive, he kidnapped her.
Lois was pregnant at the time and close to her due date. Realizing that she was in danger, Kal took her to the Batcave, knowing that Thomas Wayne was a doctor. By that point, Lois' contractions had begun and she had no other choice but to deliver her baby in an alternate version of the Batcave.
Superman arrived shortly afterwards to help, asking for Wayne's assistance because of his history as a doctor. Unfortunately, this version of Batman was still scarred from his earlier experience of losing his son, Bruce. He explained he hadn't practiced medicine since Bruce died in his arms, but he sympathized with a father fearing for his child, so he allowed the Kents to use the equipment and safety of the Batcave to deliver their baby.
Over the next few hours, Superman worked to help Lois bring their son into the world. All the while Thomas stood guard, the lethal vigilante now being a protector of sorts as Superman's attention could not be on the rest of the world. And thus, Jon Kent was born with some assistance from one of the multiverse's deadliest versions of Batman.
Eventually the new family of three would migrate to the New 52 universe, where they existed parallel to that version of Superman and Lois. This created some confusion as it became more and more apparent that this was not the world they were accustomed to. Fortunately, during the "Superman Reborn" story arc, Jon managed to help merge the timelines of both versions of his parents. This altered how he came into the world, but kept some aspects of it.
In his new origin story, Jon was conceived shortly after his parents got married. Wishing to give his wife a safe place to deliver their baby, Superman relocated her to the Fortress of Solitude. There, with the assistance of Kelex, they delivered infant Jon while Batman and Wonder Woman stood guard outside of the Fortress, making sure nothing and no one would ruin this special day for their friend.
It was a more simplified version of the birth, yet it retained the part about Batman helping to make things easier for Clark. The strength of the bond between Superman and Batman was in this way capable of crossing multiverses and different timelines.