This phrase is from the perplexing book Valis by Philip K. Dick. Read the node, read the book.
At first it seems that this is a fairly obvious (for a Dick book) reminder that the Roman Empire, a manifestation of the Black Iron Prison, which is itself a manifestation of the sickness of our universe Yurugu, has not actually collapsed. It did not actually collapse because the break-up and fall of the Roman Empire occurred during the simulation of time created by the Black Iron Prision after time stopped because of the sacking of the Temple of Jerusalem (70 AD). Time only restarted in 1974 when Horselover Fat had his first encounter with VALIS. What happened during this time did not really happen.
Upon closer inspection, the phrase appears to have deeper meanings. Wouldn't you just know it. The Empire, as noted above is a manifestation of the sickness of our universe, which is called Yurugu. Thus when it is said that the “Empire never ended” we are also saying that the sickness of the universe has never ended. This is an important fact to remember, which is why Fat uses it so often.
“The Empire never ended” is entry 6 in Fat’s Tractates Cryptica Scriptura. It is scattered liberally through the rest of the Tractates Cryptica Scriptura, featuring (usually at the end of the entry) in entries 15, 20, 21, 25, 29, 40, 45, and 47. Elsewhere in the book the phrase always appears in inverted commas, presumably because it is being quoted from the Tractates Cryptica Scriptura.