The most popular part of the Metal Gear franchise, the MGS sub-series began with Metal Gear Solid, which was named as such to indicate the move to 3D graphics. While the gameplay and plot elements remained largely identical to its 2D predecessor Metal Gear 2: Solid Snake, MGS's biggest leap was in terms of presentation, relying on fully-voiced 3D cut-scenes to present the cinematic narrative, not to mention the addition of an early cover system.
However, the MGS series didn't truly differentiate itself from its 2D predecessors in plot and gameplay terms until Metal Gear Solid 2: Sons of Liberty, which expanded the gameplay significantly and subverted the traditional narrative formula of the series, with Metal Gear Solid 3: Snake Eater subsequently changing things up even further.
The overarching theme of the initial MGS trilogy is that of "Gene, Meme, Scene". Metal Gear Solid deals with genetics and the moral implications of genetic engineering, Metal Gear Solid 2: Sons of Liberty deals with how identity can be affected by the philosophies of one's society (a 'meme') and the effects of censorship on society, and Metal Gear Solid 3: Snake Eater deals with how the time and place one lives in (a 'scene') affects their identity and how politics change along with the times