The National Intelligence Service reportedly raised doubts over the religious convictions of suspects, describing them as Muslims who “preach water while drinking wine".

A report seen by The Standard places the late Harun Fazul at the top of the list of terror suspects.

Omar Awadh Omar, aka Abu Sahal, comes in second place.

Fazul was linked to a man identified as Bilal El Berjawi and another one listed with only one name, Badrudin, who was described as the head of Al-Qaeda Intelligence in Nairobi.

Besides Fazul and Omar were 12 other names, with Jabir and Mohamed Ali listed as key missing persons.

Those on the list are Hussein Hassan Agade aka Gogo; La Tanga aka Prof aka Muhadir (formerly Alex Lishama Agade); Issa Ahmed Luyima aka Abu Zargawi; Sheikh Idriss Magondu aka Doctor (formerly Christopher Magondu); Hijjar Nyamadondo Selemani; Salim Hassan Ali aka Salim King; and Abubakar Batemyeto aka Nsimbi.

Others are Hamid Mohamed Suleiman aka Abu Zeinab of Nairobi Cell; Yahya Suleiman Mbuthia aka Yasul; Habib Suleiman Njoroge aka Bibu aka Bibs aka Abu Aiman aka Mzee aka Mzwanda, and lastly Musa Hussein Adbi aka Musa Dheere.

Somali forces shot dead Musa Dheere, an explosives expert who used an artificial leg, together with Fazul (who was on the Federal Bureau of Investigation (FBI) list of wanted terrorists) at a roadblock in Mogadishu in June 2011.

Seven out of those listed in the intelligence report are currently in Uganda’s Luzira Maximum Prison facing terrorism and murder charges in Ugandan courts.

The document described Omar as a “Nairobi-based second-hand motor vehicle dealer (who) has emerged as the undisputed leader of the Al-Qaeda cell in the region, filling in the void created by the death of fugitive Harun Fazul.”

The operationally-savvy Omar, the document states, was said to be close to slain preacher Sheikh Aboud Rogo.

He is “alleged to have provided accommodation for Al-Qaeda and Al-Shabaab elements and facilitated travel of foreign recruits to Somalia,” the report states.

Omar was accused of co-ordinating the treatment of fighters injured in Somalia, co-ordinating finances and communication links, recruiting and indoctrinating members and supporting planned terrorist attacks.

He is further alleged to have provided accommodation for Al-Shabaab suspects Saleh Ali Saleh Nabhan, Issa Osman Issa and Danish Mohamed Muhudin Gelle aka Jibril.

Issa is alleged to have been a key player in the 2002 Kikambala (Mombasa) attack before Omar facilitated his travel to Sudan in 2007.

Jibril was arrested in Denmark after a foiled attempt to attack a cartoonist who drew caricatures of Prophet Mohammed that sparked international condemnation by Muslims.

Omar is said to have facilitated the travel of foreign recruits to Somalia, namely British nationals Bilal El-Berjawi and Mohammed Sakr, and three Moroccans, Nadane Si Mohamed, Brighit Mohamed and El Adlani Moulay Abdel Halim, who were arrested in El-Wak before entering Somalia.

He also facilitated travel for two Tunisians, Hamza Mohamed Hersi and Ben Mansour Mohamed, and Sudanese Idriss Ibrahim Ali who were arrested in Nairobi’s Eastleigh.

Omar allegedly co-ordinated the travel and treatment of Ahmed Abdulahi Hassan aka Anas, who was injured while fighting near the presidential palace in Mogadishu in 2009.

A Nairobi FBI source said Omar often referred to his Kikuyu errand boys as “my niggers". However, the report fails to provide tangible evidence against most of the suspects who are termed “suspects of the Kikambala bomb attacks”, only stating that they are close associates of Omar.

The intel brief states that Hamid Mohamed Suleiman “undertakes logistics and runs errands for Omar, including movement of foreign recruits to the Somalia border. Yahya Suleiman Mbuthia and Idriss Magondu run “logistics”, while brothers Habib Suleiman Njoroge and Hussein Agade were trained in Somalia and were involved in transporting suicide vests to Kampala.

I travelled to Kireka, a city suburb and the place where Omar says he was first taken while in Uganda, where he was briefly detained in safe houses. He claims Uganda’s various security and intelligence agencies keep safe houses for undercover operations.

“Omar, look around. This is a military barracks. If you move, even to scratch yourself, we won’t think twice about shooting you.”

These are the first words Omar recalls an officer telling him in Kireka. The suspects claim they were moved from one safe house and detention centre to another.

“You can be put in a van and then moved around,” a security agent told us. Uganda’s methods to extract the “truth” from suspects are told in fear. In some safe houses, suspects are said to be threatened with snakes while others are said to have died from snake bites and other methods of torture.

During the interrogations, Omar says he was taken in shackles to face a team of Caucasian interrogators wearing civilian clothes. In court documents, he described the third interrogator as one who seemed “to have considerable knowledge about Kenya and spoke Kiswahili".

“I asked the interrogators who they were and in reply one of the white interrogators told me they were from the FBI,” Omar claims,  even though the man appeared to have an English accent.

During the questioning, according to court documents, there was also a very muscular white man and a Kenyan officer, whom Omar recognised. No lawyer was present.

The quizzing started with Omar being called a terrorist and a bastard. When he complained that the handcuffs were tight, the interrogators tightened them more, causing him extreme pain.

“I was forced to sit on a small hard stool which had wheels like a secretary’s chair but it had no back so the interrogators pulled me back and forth,” he says.

“One interrogator would grasp the back of my neck very tightly if he was not satisfied with my answers and drag me around on the stool while clutching my neck,” he recalls.

The questions he was asked included who he knew in the UK. Omar claims an FBI agent said to him, “It’s unfortunate that you are not part of the group involved in the Kampala bombings, but you are from a more dangerous group,” before punching him in the back.

The coming days involved more interrogation by a man who sounded like an American but who introduced himself as Ibrahim.

“I think you’ve never tasted a bullet, have you?” A Ugandan officer called Nixon asked Omar when he declined to co-operate with Ibrahim. He then grabbed his head and stuck the gun in his mouth saying, “I expect you to co-operate fully with this man (Ibrahim).”

Omar says he was probed about 15 times in 21 days when he was in Kireka.

For the first two years, the suspects were moved to various safe houses and detention centres and finally taken to Luzira. During this time, the harsh questioning did not stop and their trial never commenced.