Split cases find Connor, Natalie, and Powell in New York City trying to cure victims who are presenting paralysis as a result of the September 11 Terrorist Attacks, and Miles and Eva down south trying to figure out what is causing the pregnant wives of military men to miscarry.

The NIH team teams up with the officers of the 55th Precinct in New York City to try to figure out what is the source of an outbreak of Marburg, a deadly disease with no known cure. They also try to locate patient zero, a murder suspect on the run, who is helping to spread the disease throughout New York City. The crossover starts on Third Watch S06E16 In the Family Way (I)

A smallpox outbreak sends the NIH team to Montana. However, is this once thought to have been eradicated disease caused by terrorism, or is it natural?

The team travels to Baltimore to help stop an outbreak of the plague, a disease that wiped out much of Europe in the middle ages. But they uncover a string of dirty cops, who were trying to cover up a murder, in the process.

When people in New York City start turning the color blue, the NIH team is called upon to help cure this outbreak. When searching for the cause, a diner holds an important clue.

An ""Angel of Death"" runs amok in a hospital, spreading a deadly flesh eating virus, which kills patients. Now it is up to the NIH to stop this lunatic, who has a past that they should not be proud of.

The team is trapped in a snowstorm in the arctic while trying to figure what is causing pneumonia in patients that also causes psychosis. To make matters worse, one of their own goes down with the same illness.

When a couple of Iraqi War vets start showing signs of Gulf War Syndrome, the NIH team is called to investigate. However, when a group of Nursing-home residents fall ill with the same symptoms, the NIH team is left baffled. However, they are missing the bigger picture, where a lector holds an important clue.

After the victims of a car accident are diagnosed with a deadly disease, which caused the accident, a small Maryland town requests the assistance of the NIH team. The only problem is there is only one living victim, as the other nine victims had perished, and in order to save her life, and find the cure, she requires a bone marrow transplant. This little girls runs out of luck as her father has died from the same disease and her mother died from a drug overdose. However, Natalie does some DNA tests to see if the bone marrow can still be used, and discovers the girl was adopted. Eva then then goes and searches for the girl's birth mother, who wants no part in the girl's life. After some tough convincing, Eva gets the mother to donate, and saves the girls life. Now, in order to find the cause for the epidemic, the team must look to some tainted seafood for the answer.

When the adult film stars in Los Angeles start falling prey to a devastating disease, the hospital summons the assistance of the NIH team. At first, being as they are adult film stars, Connor suspects an STD. However, when the perfect housewife also falls prey to the same illness, a new link is needed to be found. After some testing, it is discovered that all of the women used the same plastic surgeon for breast implants. The team contacts the doctor, who is reluctant to help, but finally convince him to abide. The team tests the implants, but finds nothing. After some tough thinking, the team realizes that some fish and some water hold the answer.

A group of four teenage girls are suspected of having an STD when they are hospitalized for seizures. However, the NIH team must uncover the true cause of the seizures, and a pair of pants holds a clue.

When the jocks of a Midwestern College start falling prey to a crippling disease, the NIH team is summoned to investigate. At first, the suspected agent is Multiple Sclerosis. However, when the coach, as well as some sorority pledges fall ill with similar symptoms, the NIH team is baffled. As it turns out, the girls are not suffering from the same illness. The common links are discovered, and for the jocks, an athletic banquet holds the answer, and for the pledges, a tube of foreign lipstick holds the answer.

Connor suspects terrorism when two congressmen and an officer fall prey to an unknown disease. However, when the leader of a prostitution ring becomes ill with the same symptoms, an unknown STD becomes the suspected agent. Now it is a race against the clock, and their pesky boss, Dr. Ewing, to find a call girl who may be the source of this deadly outbreak.

Connor and Powell must travel to a small Mexican town after an earthquake strikes, trapping Natalie, Eva, and Miles. Only when they go after Miles, who was trapped in the church Mission La Roca, they are captured by insurgents.

After years of watching young children fall prey to a crippling muscular ailment, a small community summons the NIH team to hopefully find a cure. At first, Connor suspects a local chemical plant as being the cause of this devestating. However, a common link is discovered, and the DNA of the children holds an important clue.

The team flies to a small Virgina town to figure out why people are dying from a deadly strain of the flu.

The team figures out that they are dealing with bacterial meningitis, and the only thing that makes their day worse is a corrupt politician who steals the medicine and holds it at ransom. Elsewhere, the people at Mission La Roca (Miles, Connor, Powell, Nestor, Juan, Kris, and Baracas) make it out before the church collapses, and take the sick ones off to the hospital for treatment.

The team flies to Philadelphia to figure out if Anthrax is showing up as a result of terrorism or not.

A surfer and volleyball player from a seaside town catch a mysterious disease. Dr. Connor and his staff begin suspecting that nearby seals played a part in this illness, however are the other forces at play?

When the vacationers in a Bahama resort start falling ill, the NIH team is called in to discover the cause of this devastating illness. The only problem is that this disease is not effecting the children. However, when the first child falls ill with the same symptoms, the common link is found, and an illegal drug holds a clue.