The Martians are a highly advanced alien race from the planet Mars (hence the name) that wish to invade Earth in order to conquer and colonize the planet for its resources to save the martian race from exitinction at the cost of every human life. NERV and the Evangelion pilots encounter the second invasion force, which has learned from the mistakes of the first invasion force which died from being exposed to Earth's bacteria.
In the end of the 1800s, strange clouds of mist generate from Mars and headed towards Earth, which are really cylinders. The cylinders land in Horswell common in England and later tripods emerge and begin to invade and exterminate or harvest the population. However over time as hope was lost the Martian force died of being exposed to Earth's bacteria, which the Martians were not able to combat due to having virtually destroyed all diseases on Mars.
Nearly a century later the Martians begin to invade again with better technology and knowledge. They plan quickly due to the Angels, an enemy they encountered a long time ago having been destroyed but an apolictic event that would decimate the planet of it remaining resources. However they must deal with Earth's advanced mecha, the Evangelions.
Martian technology is extremely advanced, even more than that of what NERV and SEELE have created. The tripods have increased in size since the first invasion from 80ft to 100ft tall with only the Evangelions being the only known equivalent.