The inputs are read into an input mimic area at the start of the scan, and the outputs updated from the output mimic area at the end of the scan. There will be an area of memory reserved for internal signals which are used by the program but are not connected directly to the outside world (timers, counters, storage bits, e.g. fault signals, and so on). These three areas are often referred to as the data table (Allen Bradley) or the database (ASEA/ABB).
This data area is smaller than may be at first thought. A medium-size PLC system will have around 1000 inputs and outputs. Stored as individual bits this corresponds to just over 60 storage locations in a PLC with a 16-bit word. An analog value read from the plant or written to the plant will take one word. Timers and counters take two words (one for the value, and one for the preset) and 16 internal storage bits take just one word. The majority of the store, therefore, is taken up by the fourth area, the program itself.