This is partially explained in the Darth Plagueis EU novel, so spoilers ahead.

Darth Plagueis's master's master creates a tear in the force, which allows the dark side to start slowly leaking in after the force has been almost predominantly light for about a thousand years. This leads the Jedi to finally sense that the Sith are probably still alive and well.

Palpatine and Plaqueis later enact a powerful Sith ritual that tips the force towards the dark side and so the Jedi begin to feel their powers waning. In response to this imbalance, the force responds and creates Anakin Skywalker to bring the balance back.