This species was last recorded by Andrews from his 10 month stay on Christmas Island 1897-1898 (Andrews 1900). At that time, it already appeared to be in decline. Although the species was known from the settlement at Flying Fish Cove, Andrews never encountered them there and believed they were mainly confined to higher ground (Andrews 1900, 1909). In the hills, he described them as "very numerous in places", but less common than R. macleari (Andrews 1900). Andrews (1900) states that "it is difficult to avoid the belief that the former species [R. nativitatis] is being supplanted by the latter [R. macleari] in spite of the abundance of food."
By the time Andrews revisited the island in 1908, he was confident in pronouncing the species to be extinct (Andrews 1909). In 1904, Hanitsch visited the island hoping to collect specimens of the native rats, but was unable to locate either species (Pickering and Norris 1996; see account for R. macleari for further details). Durham visited the island in November of 1901 to March 1902 and collected R. macleari and R. rattus, but was unable to obtain R. nativitatis, despite offering a reward to the local inhabitants (Pickering and Norris 1996; see account for R. macleari for further details). Pickering and Norris (1996) note that Durham did not go far from Flying Fish Cove during his stay, thus he could well have missed R. nativitatis. However, Hanitsch's failure to obtain R. nativitatis in 1904 likely means that the species was extinct by this time. Andrews (1909) relates anecdotal information that a medical officer on the island, Dr. McDougal, recalled frequently seeing "individuals of the native species of rats crawling about the paths in the daytime, apparently in a dying condition" in 1902-1904, and these may have included R. nativitatis, but were likely to be R. macleari (see account for R. macleari for further details).
The demise of the Bulldog Rat was certainly rapid, going from locally common to extinct in less than eight years. It is thought to have been the result of an epidemic disease brought to the island by introduced Black Rats R. rattus (Andrews 1909; Aplin 2008). Black Rats are thought to have been introduced to the island by the S.S. Hindustan in 1899 (Pickering and Norris 1996) - subsequently determined to be September 1900 by Green (2014). This hypothesis is supported by the study of Wyatt et al. (2008), who used ancient DNA methods on samples from museum specimens of these rodents collected during the extinction window (AD 1888–1908), and showed that endemic rats collected prior to the introduction of Black Rats were devoid of evidence of a pathogenic trypanosome (carried by fleas hosted on recently-introduced Black Rats).