All batteries exhibit a phenomenon known as ''self-discharge'', i.e. when left unused for long periods they will slowly discharge due to internal leakage currents. Usually this gets worse when the battery gets older.
A Li-Ion cell is considered to be fully discharged when the cell voltage has dropped to 3 Volts. But self-discharge might drop the voltage still further. However, most charging circuits, including those built into Li-Ion powered gadgets, will refuse to charge a battery that has dropped below 3 V, it will consider the battery as being defective.
If the cell has not dropped too far below 3 V, one might attempt to force charge the cell by connecting it to a suitable power supply and carefully monitoring cell voltage and current. Once the cell has recovered to a voltage over 3 V, the charger will usually accept it and charge as usual. However, keep in mind that Li-Ion cells are somewhat fickle and charging a defective cell may result in Bad Things Happening. So if you want to be on the safe side, it would be better to just replace the battery.