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The story is set in the year 2018, where diseases that were previously thought to be incurable are nearly things of the past.
The player assumes the role of Derek Stiles, a doctor at Hope Hospital. After initial training, Derek begins to understand the potential he possesses. Soon after discovering his power, a disease like no other begins to surface. Through many surgeries, Derek fights the unknown disease.
Trauma Center is divided into several chapters and operations within each chapter. Each operation must be completed in order to access the next one and progress through the game.
The lower screen on the DS is used to display the patient, the patient's vitals, the instruments available, and is where the operation is carried out. The top screen is used to display instructions, the time remaining, the player's miss limit and score.
A typical mission requires the player to operate on a patient. During each operation, the player must keep the number of errors committed below a set limit, ensure that the patient's vitals remain above zero and keep within the time limit. If the player runs out of time, reaches the miss limit, or the patient's vitals reach zero, another surgeon will take over the operation, which will always seem to fail.
Upon successful completion of an operation, the player is ranked based on the time remaining, the health level of the patient, and a net score based on the accuracy of the operation. The total score is then ranked, with special score rankings for each operation. Rankings for these are graded:
Rank S- Master Surgeon
Rank A- Senior Surgeon
Rank B- Specialist
Rank C- Rookie Doctor
The player may repeat any operation in Challenge Mode and attempt to earn a better grade. Three save slots are available, but only the best score is recorded for each operation.
In addition to normal operations, there are operations known as "X-missions". The X-missions are seven operations, each one containing an ultrahard version of a strain of GUILT. However, the game does not note the player about the X-missions, unlike the other games in the series. As with every game in the series, the X-missions are unlocked after beating the game once, and are found in the challenge mode, with fake records used to fill the time/score/rank slots (such as exactly 30 seconds remaining on the clock). As with every game in the series, the player is not required to complete these operations.
In the May 2008 issue of Nintendo Power, an article showed that a sequel, titled Trauma Center: Under the Knife 2 is set to be released July 1st, 2008. The game is described as keeping the same gameplay, with "some of the old ones (the surgical tools) [having] improved functionality as they did in Trauma Center: New Blood." Dr. Stiles and Angie will feature once more, taking place after the events of the first game. Reviews of the second game have been generally positive.