The cell has different parts, and those that can absorb stains or dyes are referred to as chromatic. Having absorbed the stain, these parts of the cell become more visible under the microscope and can therefore be easily distinguished from other parts of the same cell.
Without stains, cells would appear to be almost transparent, making it difficult to differentiate its parts.
Methylene blue has a string affinity for both DNA and RNA. When it comes in contact with the two, a darker stain is produced and can be viewed under the microscope.
The nucleus at the central part of the cheek cell contains DNA. When a drop of methylene blue is introduced, the nucleus is stained, which makes it stand out and be clearly seen under the microscope.
Although the entire cell appears light blue in color, the nucleus at the central part of the cell is much darker, which allows it to be identified.