The basilica had nearly been destroyed by an earthquake in the ninth century and had begun to deteriorate by the middle ages and was further harmed by two fires leading to the beginnings of a reconstruction campaign under Pope Sixtus V in the late sixteenth century. The interior itself was also reconstructed beginning in the seventeenth century under the watch of Francesco Borromini, and this is the interior that we are familiar with today.
In the first millennium, the basilica had been so enriched and beautified by gifts from popes and emperors, it earned the nickname, "Basilica Aurea" or golden basilica. Regrettably, this made it the target of attack and looting under the vandals who stripped it of its treasures.
The question that naturally arises with all of this historical lineage, much like it does for St. Peter's, is, "what did it look like before?" Evidently a basilica of this age is bound to have undergone various programmes of restoration and renovation as the centuries pass, whether for reasons practical or stylistic, but if you want to get a sense of the pre-Borrominian interior of the archbasilica, you can see it depicted here following.
Many are quite well aware of the "scavi" (excavations) that can be found beneath St, Peter's Basilica (a ticket well worth its price if you wish to see the Roman ruins and original location of St. Peter's relics), but what many may not be aware of is the fact that there are a similar series of excavations taking place beneath St. John Lateran for the Lateran was also built overtop a series of Roman era buildings, ranging from Republican era palatial residences, to Roman buildings that housed the imperial horse guard.
Here is a closer look at one of the underlying structures that can still be found, including the remnants of Roman era frescoes.
Readers interested in this kind of archeology may wish to read our similarly themed article, What Sits Underneath St. Peter's Basilica in Rome.