  We use six, high-resolution $\Lambda$CDM simulations of galaxy formation to
study how emission from dark matter annihilation is affected by baryonic
processes. These simulations produce isolated, disc-dominated galaxies with
structure, stellar populations, and stellar and halo masses comparable to those
of the Milky Way. They resolve dark matter structures with mass above $\sim
10^6$ $\rm M_{\odot}$ and are each available in both full-physics and
dark-matter-only versions. In the full-physics case, formation of the stellar
galaxy enhances annihilation radiation from the dominant smooth component of
the galactic halo by a factor of three, and its central concentration increases
substantially. In contrast, subhalo fluxes are $reduced$ by almost an order of
magnitude, partly because of changes in internal structure, partly because of
increased tidal effects; they drop relative to the flux from the smooth halo by
1.5 orders of magnitude. The expected flux from the brightest subhalo is four
orders of magnitude below that from the smooth halo, making it very unlikely
that any subhalo will be detected before robust detection of the inner Galaxy.
We use recent simulations of halo structure across the full $\Lambda$CDM mass
range to extrapolate to the smallest (Earth-mass) subhaloes, concluding, in
contrast to earlier work, that the total annihilation flux from Milky Way
subhaloes will be less than that from the smooth halo, as viewed both from the
Sun and by a distant observer. Fermi-LAT may marginally resolve annihilation
radiation from the very brightest subhaloes, which, typically, will contain
stars.
