Ilija is a member of the Croatian Defence Council (HVO) somewhere in Central Bosnia in late 1993. One morning, after a routine mine laying campaign, he learns his younger brother Goran was killed far beyond enemy lines, together with eight other soldiers. Through a friend from the secret service, he finds out the mission was an unofficial one and that Goran and the others were acting as mercenaries. Ilija begins to expose a network of illegal activity involving not only the military, but high-ranking officials. As the investigation becomes more dangerous, his original intention to find out the truth slowly turns into a pathological mission of vengeance.

Don Fabijan is a young priest who comes to serve on an unnamed small island in the Adriatic. In order to help increase birth rate on the island, he decides to pierce condoms before they are sold. He therefore teams up with the newsagent Petar and the pharmacist Marin. After they abolish all forms of birth control on the entire island, the consequences become more and more complicated.

In 1943, group of Croatian soldiers overtake a strategically important point in western Bosnia with a goal to destroy a group of communist partisans. On the way they met some supernatural phenomena, and the action itself went very badly because the partisans ambushed them. The main character Martin inherits silver cigarette case from a dying soldier. This act connects to the story in 1993 when we meet Martins grandson Tomo. He is one of six soldiers of the Croatian army who have come to the same place in Bosnia to meet the same phenomena and similar fate.

Set amid the atrocities of war in the Balkans, Witnesses is retold, Rashomon-style, from various characters' viewpoints, adding new information about the complexity of war and humanity. Beginning inside a rustic house with a woman in black (Mirjana Karanovic) standing beside her husband's coffin, Witnesses interweaves the stories of a small town confronting ethnic hatred and deep moral ambiguities.