Enterprise is asked to evacuate a group of Denobulan geologists from Xantoras, a world that has been taken over by a militant faction. The Denobulans are located in some underground caverns, so the rescue team — Mayweather, Trip and Reed — will have to traverse some treacherous rock formations in order to get them out. Meanwhile, another ship of off-worlders is headed away from Xantoras when their reactor casing is ruptured, flooding the ship with radiation. When the Xantoran officials refuse to let the ship land, Archer agrees to bring the evacuees onboard Enterprise for treatment. One of the evacuees is an Antaran named Hudak, who is horrified that Enterprise's doctor is Denobulan. Phlox explains to Archer that the Denobulans and Antarans have a troubled, bloody history between them — the two species have gone to war several times. Even though it's been three hundred years since the last conflict, much bad blood still exists between them.
As it turns out, Hudak has absorbed a heavy dose of radiation and will need a medical procedure in order to live. Hudak, however, refuses to be treated by a Denobulan, and Phlox won't treat a patient against their wishes. Archer threatens to order Phlox to do so, but the doctor stands firm — he will not treat the Antaran until Hudak gives his consent.
Meanwhile, Trip, Reed and Mayweather are attempting to navigate the treacherous caves on Xantoras. Mayweather is a skilled climber, and attempts to teach Reed and Trip various techniques. Unfortunately, the trio suffers a dangerous fall, and Mayweather injures his ankle. As he cannot proceed, Trip and Reed continue on without him and eventually locate the Denobulan geologists. The geologists, however, are unwilling to leave. Their research is going very well and they've collected many important rock samples.
On Enterprise, Archer tries to convince Phlox to set aside his preconceptions and attempt to get through to Hudak. If the Antaran doesn't receive the necessary treatment soon, he will die. Phlox attempts to make conversation with Hudak, but Hudak isn't interested. He asks Phlox if he ever told his children stories about evil Antarans, or taught them to be afraid of the Antaran people. Hudak's harsh words cause Phlox to examine his own upbringing — he remembers being taught to hate Antarans, and was determined not to raise his own children the same way. He tells Hudak that he tried to educate his children, to raise them so they wouldn't be prejudiced against other species. He also reveals that his son Mettus did end up embracing hateful, anti-Antaran values, and that this has created a rift between father and son. In the end, Phlox's words move Hudak, and the Antaran can't help but think of his own children. He agrees to go through with the procedure.
Meanwhile, a frustrated Trip has finally convinced the Denobulan geologists to leave the cave. As the caves are rocked by nearby fire, Archer discovers that a Xantoras patrol has opened fire on soldiers from a previous regime. Archer manages to convince the Governor of Xantoras to stop firing until Trip and the others return to Enterprise. They escape just in time, and the Denobulan geologists are brought safely onboard.
Having successfully recovered from the treatment, Hudak prepares to leave. Archer sees him off, informing him that the Denobulan geologists will be joining Hudak on the transport. Hudak is cautious, but seems more open to the idea than he would have previously. As Hudak heads off, Phlox sits in Sickbay, penning a letter to his son. He expresses that a recent experience has changed him and he hopes his son will listen. Perhaps it's the first step in re-building a bridge between a father and his estranged child.