The core site is the execution site at the museum and houses the following mini sites

Core Site
Mukaajaanga's Command Post

This is the house where the chief executioner called Mukaajaanga lived when he was in Namugongo on official duties. In this house was his equipment: the spears, swords, clubs sticks, harmers, axes drums, knives, ropes etc. Mukaajaanga also hosed his drinks (local brew) in this house.

Core Site
Preparation Site

Between Mukajanga's house and "Ndazabazadde" tree, there was a place where Mukajanga's men sharpened their swords or knives before they killed the prisoners.

This is where 5 - 6 men usually sat and sharpened and washed their knives, spears, harmers, axes and clean the clubs as a way of instilling fear into the Christian converts. It was also a way of teasing their victims who were awaiting execution.

Core Site
Prison

This was a cell where the prisoners were kept until the time of execution came to pass. Some even died of hunger or thirst while in this prison. They always sat down with their legs stretched out tied together at the ankles to curtail movement.

In the prison, prisoners were tied with sticks around their legs, which made prospects of escaping hard.

Core Site
Namugongo (Dragged by the Back)

This section dramatizes the genesis of the word Namugongo. Namugongo is derived from a Luganda word "Omugongo" or "backside of the human body - The people or subjects were dragged on their backs by the royal guards, Mukaajaanga's men, when there were on their dreadful journey to meet death at Namugongo.

Core Site
Ndazabazadde (Torture Tree)

This is tree under which the prisoners were tied them tortured and at times dismembered with their eyes plucked out, fingers, legs, hands cut off and left to die slowly. The mothers of the victims taken for execution used to bravely follow and would lament, cry on seeing their children suffering and being tortured on this tree.

They would painfully cry out that "Endazabazadde zirabye, n'olumwa ng'ozaala, ate n'olaba omwanawo nga akaaba nga bamutta!" literally meaning that mothers go through pain when giving birth and them feel the pain inside watching their sons suffering and brutally being killed on the dreaded tree. As a result of this, the dreaded torture tree was nicknamed Ndazabazadde.

Core Site
Firewood Heap

This is a site showing a heap of firewood that was used to fuel the menacing burning pyre onto which the martyrs were put and burnt to ashes.

Core Site
Burning Site

After torture, Mukaajaanga instructed that the Christians be tied between racks; arranged embers of fire atop fireplaces which had been already made. They lifted the racked victims and put them atop embers and put more wood atop them and set the martyrs ablaze.

Core Site
The Tomb Site

The martyrs church or chapel is where the remains and the bones of the martyrs were buried. A chapel was built at the site to commemorate the bravery of the Uganda martyrs. The alter inside this chapel was built on the tomb in which the remains of the 25 Martyrs (13 Anglicans and 12 Catholics) were buried. This chapel has been well preserved with a roof built to protect the site from weather hazards.

Core Site
Martyrs' Memorial Spring Well

After executing the prisoners Mukaajaanga the chief executioner and his aids would then descend down to the well and wash off the blood and sweat while at the same time cleaning their instruments.

Their bathing in this well was another way of cleansing their bodies of guilt. For they would then call on the spirits of the departed victims not take them responsible for the death but to blame it on a spirit medium Nende. Nende was the Buganda spirit medium responsible for the boundaries of the kingdom, protection of the king and the King's wishes.