Stars are responsible.
HII regions$^dagger$ can refer to several things, but usually I guess one thinks of the volumes around star-forming regions. The more massive a star is, the faster it burns its fuel, and at a higher temperature, meaning that the peak of their spectra are more toward the high frequencies. The most massive stars of a stellar population — the so-called O and B stars — produce enough photons with wavelengths below the hydrogen ionization threshold of $lambda = 912$ Å that they carve out bubbles in their surrounding HI clouds, giving rise to HII regions.
Right: The HII region NGC 604 (from Wikipedia). Left: The spectra of three different stars. Only the B star has a significant portion of its spectrum above the hydrogen ionization threshold. Note the logarithmic scale on the intensity (from here).
Because of the high densities, the HII quickly recombines to HI. If the recombination goes directly to the ground state, a new ionizing photon is emitted, which again is absorbed by a hydrogen atom, but if it goes to one of the higher states, the emitted radiation is no longer capable of ionizing the gas. In this way the ionizing radiation is converted into photons of specific wavelengths, corresponding the energy differences between the excited level of hydrogen, most notably the Lyman $alpha$ emission line with $lambda = 1216$ Å.
Because hydrogen is the most abundant element in the Universe, and because Lyman $alpha$ is the most common transition, the Lyman $alpha$ line is an excellent probe of the most distant galaxies where other wavelengths are not observable. This is especially so because the most distant galaxies are also the earliest and hence still in the process of forming, meaning a high star formation rate which, in turn, means that the shortlived OB stars are still present.
In addition to this distinct regions of HII, ionized hydrogen also exist in a more diffuse component between the stars of a galaxy, in huge bubbles caused by stellar feedback and supernovae, and in the intergalactic medium.
$^dagger$The terms HI and HII refers to neutral and ionized hydrogen, respectively.
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