I really love the Zombie Apocalypse Mod I have for F3, which I downloaded from the Fallout 3 nexus site.
Now I thought it would be a neat idea to bring back the Aliens into Fallout New Vegas but with an additional story: Zombies.
The story could be something such as this:
Just before the Aliens aboard Mothership Zeta were defeated, a distress signal was send out to their brethren back on their home world.
Another ship was sent out to come to the aid of Mothership Zeta, and arrived in our solar system some time later.
The Alien's expeditionary force learned what happened to their brethren and began immediately to devise plans on how to avenge their comrades as well as how to destroy mankind and conquer earth thereafter.
Rather then initiating a full scale attack on earth, they instead establish a secret base of operations in the Mojave desert.
They do not intend to fight an open war, but instead create a biological weapon, a virus, with which they infect abducted test subjects within their deep-subterranean base ( humans, ghouls, Super Mutants etc....) and later on release these abductees ( whose memory of the abduction got wiped ) back out into the open to infect others.
The virus basically works like the virus from 28 days/weeks later.
Our hero's quest is basically to find out what is causing the outbreak of Zombies.
He/she would have to do some quests to learn more about the Virus and the Zombie Outbreak from different factions, fight hordes of Zombies while doing so, aid factions in battle against the undead/enraged infected and would eventually learn the origin of the virus and who is behind it.
From battles with zombies in settlements, the desert, Vegas and military bases, all the way to the Alien base.
Anyways, I think this would make for one hell of a Mod or DLC ( lol I am hopping someone from Bethesda reads this and is inspired =P )