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In 1906, Colonel Hatch receives orders that the American troops he leads are to withdraw from Fort Mysang on the Philippine island of Mindanao.  Hatch protests, saying that Alipang and his Moro bandits will overrun the other natives, but his commanding officer tells him that he will have to train the natives to defend themselves before he leaves.  To accomplish this goal, Hatch receives aid from a team of specialists: Doctor Bill Canavan, Lieutenant Terrence McCool, Captain Steve Hartley, Lieutenant Larsen and Captain George Manning.

Alipang watches as the men arrive at Mysang and orders one of his followers to kill Colonel Hatch so that the unprepared native troops will be goaded into attacking his forces in the jungle, and be slaughtered.  The assassin is successful, and despite Canavan's attempts to save him, Hatch dies.  Hartley receives a head wound during the attack, but recovers and becomes second-in-command to Manning.  While native Lieutenant Yabo and the Americans struggle to train the native troops, whose fear of Alipang debilitates them, Manning prepares to welcome his visiting wife.

On the boat with Mrs. Manning is Hartley's daughter Linda, whom he has not seen in four years.  Linda's visit surprises her father, and even more surprising is her determination to stay with him.  She quickly becomes the focus of a romantic rivalry between Larsen, McCool and Canavan, but she seems to prefer the tough yet understanding doctor.

On the night of the women's arrival, Manning falls prey to another of Alipang's assassins, and Hartley, who is going blind from his head wound, assumes command.  With the help of Miguel, a Moro lad who is loyal to the Americans, Canavan captures one of Alipang's men and ridicules him to dispel the native troops' fear of the Moros.  Conflict grows between Canavan and Hartley, who resents the doctor's dismissal of his orders as childish and fear-driven.

Determined to lure the troops into the jungle, Alipang dams the river that flows through the village, and as the villagers are forced to use unclean water, a cholera epidemic breaks out.  While Linda helps Canavan treat the ill, Miguel and Larsen lead a group of men to dynamite the dam.  When they do not return, the Datu, a Moro chieftain secretly in league with Alipang, offers to lead Hartley and the troops to the dam.  After they leave, Miguel returns alone, badly injured.  He tells Canavan that the Datu killed Larsen, and the doctor rushes to warn Hartley.  He catches up with the troops as they are being lead into an ambush, and sends them back to the village while he goes to the dam.  Canavan succeeds in dynamiting the dam, but as the villagers are celebrating, they are attacked by the bandits.  While Canavan orders the troops to build rafts with which they can reach the fort quickly, McCool is killed defending the ammunition stockpile.  The doctor reaches the fort first and, along with Linda, defends against the marauders until the troops arrive.  Yabo's men are victorious against the Moros, and peace is established in the region.

Later, Hartley, Linda, Canavan and Miguel board a ship bound for home, and Yabo and his men proudly salute them goodbye.