The cover is the idea that it can track the animal from birth to food supply but the main problem is with the big producers which are the ones that make it so a hamburger can contain not just twenty cows but from that many countries as well (part of their issue with COOL). Big Ag would ironically be mostly exempt and would get a huge financial advantage by being able to register their animals as lots rather than individually.

As I understand it the NAIS would require a microchip the cost of it alone could add $15 to each chicken (though for the big producers it's just one lot) and then massive amounts of paperwork including computer and internet tracking (or facing huge fines and jail time) if the animal moves at all including to fairs, or as in the case of a horse, every time it is ridden off property.

Besides pushing regulation and costs up to drive out small producers which would force people to purchase from the top companies, it is also believed that it will have the government coming in and destroying small farmers entire livestock supplies without compensation because there was rumor of an outbreak in one of the disease factories the big companies run. Not to mention that diversity is the key to diverting devastating losses due to disease and that it's the big crowded conditions not the small farmer where outbreaks fester. Nice way to quickly take out the competition.

As far as any tracking, the technology is already there. The industry doesn't want to be held accountable and won't let independents test their animals for things such as Mad Cow because that will harm the mainstream supply which avoids testing.

Here's the intro on the NAIS Story at Liberty Ark:

If fully adopted and implemented, the likely outcome of NAIS is that animal ownership increasingly will be limited to large entities who can afford to comply and who are willing to accept the governmental intrusion. Yet this "feel good" program will do virtually nothing to safeguard animal health, its alleged purpose. Rather, NAIS will do all of the following:

- drive small producers and their supporting suppliers (feed stores, auction houses, etc) out of existence

- make people abandon raising animals for their own food and as pets

- invade Americans' personal privacy to a degree never before tolerated

- deprive Americans of their property rights

- violate the religious freedom of Americans whose beliefs make it impossible for them to comply

- cost the American economy far more than it will deliver

So what is this program and how did it develop?

History

The concept of an electronic national animal identification system was started back in the early 1990s, by technology companies seeking to expand their market, and large agricultural entities seeking to protect their ability to sell their mass produced meat on the world market.

Their efforts culminated in 2002, when the National Institute for Animal Agriculture (NIAA) proposed that the USDA develop a "national animal identification system" (NAIS). While NIAA may sound like a public interest organization, its membership reads like a who's who in industrial agriculture and technology, including entities such as Cargill Pork, Tyson, National Pork Producers Council, and Global Vet Link.

Notably, the NIAA developed the national animal identification system more than a year and a half before the first case of Mad Cow was found in the U.S. Over the course of three years, USDA and NIAA worked together to develop the NAIS and inform the large-scale livestock producer community, while ignoring hundreds of thousands of people who will be affected.

From what I have read on the most recent Foot & Mouth outbreak, it was an issue with a couple labs letting the virus loose and not the animals spreading it.