We shall just have to open up more Helium mines.
Helium is a product of radioactive decay of a number of different transuranic elements, an inert “noble” gas that is the second lightest of elements in the Universe (after monatomic hydrogen, which does not exist in natural form).
Helium is being formed all the time in the molten core of Earth, and is a major constituent of the mass of the sun and every star, as it is very much a part of the evolution of elements. In the hellish cauldron that is at the core of these many stars, it is a building block of the entire rest of the periodic table as the enormous pressures and heat press the protons at the nucleus of every atom close enough together they then fuse into a new larger, heavier nucleus.
Because of its very low molecular weight, once helium gets into the open atmosphere, it rises in the atmosphere until it escapes earth’s gravity altogether and is lost forever, scattering into otherwise empty space.
Monatomic Hydrogen certainly exists in nature; it is in fact the most abundant form; in fact monotomic hydrogen is the most abundant molecule in the universe; Helium is a distant second. If you mean it doesn't exist outside of stars, sure. But there's nothing "unnatural" about the sun.
Diatomic hydrogen, like Helium, would all have left the atmosphere long ago, but Hydrogen is chemically reactive, unlike Helium so it's locked up in hydrides, hydroxides, and other forms. Diatomic hydrogen in our atmosphere is produced by the hydrolysis of the ocean surfaces by sunlight.