In 1991, Cardinal Otunga became ill, and asked Pope John Paul II to resign. The Pope did not accept his proposal, but gave him a Coadjutor in 1996, in the person of Bishop Raphael S. Ndingi Mwana’a Nzeki of Nakuru, who would succeed him automatically at the time of retirement or death.The following year, he suffered a stroke which prevented him from further exercising his office as Archbishop of Nairobi. His Vicar General wrote on his behalf a second letter of resignation to the Pope, who this time accepted his resignation.
With a great sense of dignity and humility, Cardinal Otunga spent his final years at Nyumba ya Wazee, a home for the elderly in Kasarani (Nairobi) operated by the Little Sisters of the Poor, asking to live like any other patient in it. There were those who objected to his choice and counseled that he should retire in a mansion or in the Vatican. The Servant of God explained his choice in this manner: “I do not wish to be a burden to anyone, nor to appear to have any other home or family apart from the Archdiocese.”
Cardinal Otunga continued to welcome with authentic hospitality anyone who visited him in Kasarani. When possible, he would come to Holy Family Basilica to celebrate the sacraments with the faithful. Abundant are the testimonies of lay persons who remembered how Cardinal Otunga, despite his failing health, consistently showed his sincere interest in personally knowing more about them and his concern for the well-being of their spouses and children.
As his health declined further in the middle of 2003, he was transferred from Nyumba ya Wazee to Mater Hospital in Nairobi. It was there that on 6 September 2003, consoled by the sacraments and the company of his brother-bishops and members of the faithful, Cardinal Otunga began his journey into life everlasting. On 19 September, thousands of mourners attended the funeral service for Cardinal Otunga at the Nyayo National Stadium. In observance of his will, Cardinal Otunga was laid to rest at St. Austin Church cemetery in Lavington (Nairobi).