The Cliff Notes version of Convergence is that Brainiac gained access to a dimensional Nexus and used it to collect cities from “dying timelines” — including Gotham City from the DCU just prior to the 2011 reboot. Superman and Lois had been visiting Gotham at the time because reasons, and got caught up in the abducted city. For a year, all metahumans in the city were rendered powerless. During that time, Lois got pregnant. Los and Clark's son (Jon Kent) was born during the events of Convergence itself, which ended with the three of them and a few other heroes being sent through time to the original Crisis to prevent the destruction of the original Multiverse. They succeeded, but ended up in the newest version of the DCU nine years in the past at the dawn of the Justice League. They've spent the last decade raising their son as depicted in Superman: Lois & Clark .
Essential reading: Convergence: Superman #1–2, Convergence #8, and Superman: Lois & Clark.