They’ll introduce alien diseases---extinction
Seth D. Baum 11, M.S., Electrical Engineering, Northeastern University, PhD student @ Pennsylvania State University NASA Planetary Science Division, “Would contact with extraterrestrials benefit or harm humanity? A scenario analysis”, Acta Astronautica Volume 68, Issues 11-12, June-July 2011, Pages 2114-2129
If humanity comes into direct physical contact with either ETI themselves or some ETI artifact, then it may be possible for humanity to be unintentionally harmed. One of the most prominent scenarios of this kind is the transmission of disease to humanity. This scenario is inspired by the many instances in which humans and other species on Earth have suffered severely from diseases introduced from other regions of the planet. Such diseases are spread via the global travels of humans and our cargo and also through certain other disease vectors. Introduced diseases have been extremely potent because the population receiving the disease has no prior exposure to it and thus no build-up of immunity. Indeed, disease introductions are blamed for loss of human life so widespread as to have altered the broadest contours of human history [83]. If ETI could introduce disease to humanity, then the impacts could be – but would not necessarily be – devastating. The disease could quite easily be significantly different from anything our immune systems have ever encountered before. The disease could also be entirely unfamiliar to our medical knowledge, and it could potentially be highly contagious and highly lethal. This combination of contagiousness (i.e. high R0 [84]) and lethality (i.e. high mortality rate) is unlikely in existing pathogens because such pathogens would quickly kill their host population and then die out themselves. Furthermore, if we had already encountered such a disease on Earth, then we likely would not be here anymore. However, a disease from ETI would be new to us. It presumably would not be highly contagious and lethal to the ETI themselves or to the other organisms in their biosphere, but it could be devastating to humans and the Earth system. Then again, ETI biology may be so vastly different from Earth biology that no significant interactions between organisms occur. ETI may have their own contagious diseases that are unable to infect humans or Earth-life because we are not useful hosts for ETI pathogens. After all, the ETI diseases would have evolved separately from Earth biota and thus be incompatible. So while there are reasons to believe that an ETI disease which affected humanity would be devastating, there are also reasons to believe that an ETI disease would not affect humanity. It is worth noting that a disease brought by an ETI could harm us without infecting us. This would occur if the disease infects other organisms of interest to us. For example, ETI could infect organisms important to our food supply, such as crop plants or livestock animals. A non-human infection would be less likely to destroy humanity and more likely to only harm us by wiping out some potentially significant portion of our food supply. In a more extreme case, ETI disease could cause widespread extinction of multiple species on Earth, even if humans remain uninfected.