Helium is generally found around stashes of uranium. When uranium decays it ejects an alpha particle, which consists of two protons and two neutrons. As soon as the particle picks up a couple of electrons, it becomes a helium atom. Because so much uranium is underground, the helium is kept in pockets in the Earth. Once it's unearthed and freed, it floats up and becomes impossible to harvest.
The loss of helium is a blow to anyone who wants an MRI done or wants to use liquid helium to cool superconductors, but it's not just the future we're ruining with our lust for party balloons — helium is instrumental in preserving the past. One of the reasons helium is useful is because it's inert. Inert elements don't interact with the elements around them, which is helpful if you want to avoid things like fire, poisoning, or corruption of materials.
Helium isn't entirely safe — it's not dangerous, unless you get stuck in a big cloud of it. Most things that gets trapped in a large cloud of helium will suffocate, including most microbial life which is why the Declaration of Independence is swimming in a cloud of helium and water vapor. The parchment needs moisture to keep from cracking, and the helium allows for the humidity that the document needs, while keeping out the oxygen that leads to decay. Most famous historical documents are stored in cases filled with helium. Which means we're going to have a lot harder time keeping our paperwork in order once the helium runs out. Guess we'll have to rely on argon and accurate transcription.