The once-boisterous little boy has lost his appetite and often sits quietly by himself, said his father.
Mr Basharath believes that Zayan understands his brother is no longer around, but has difficulty processing his emotions because of his young age.
The two were close and supposed to enrol in the same childcare centre at the foot of their Housing Board block in Bukit Panjang next year.
Mr Basharath agreed to be interviewed to share his experience with other parents who may find their children in such life-threatening situations.
It was just hours after Zaheer Raees tested positive that his condition became critical.
He first came down with a fever at about 4am on June 21, Mr Basharath said.
The family of four took antigen rapid tests to see if they had caught Covid-19 - a precaution they adopted during the pandemic whenever anyone fell sick.
The mother, housewife Septian Suci Rahayu Sartini, 31, self-isolated with Zaheer Raees after both tested positive for the virus.
While Zaheer Raees was still active later that morning, his condition deteriorated rapidly by night-time, with his temperature rising to 41 deg C.
"My wife and I, we were in panic mode," said Mr Basharath.
Leaving Zayan in the care of his grandmother, the couple called a cab and took Zaheer Raees from their Segar Road home to KK Women's and Children's Hospital.
While waiting to be admitted at the hospital, the toddler blacked out, Mr Basharath said.
When they were allowed to see him, the boy was conscious but unresponsive, only mumbling to himself.
"After a while, he started having seizures," the father said, adding that magnetic resonance imaging scans later revealed swelling in the brain.
"They (doctors) told me the brain swelling was irreversible, which means even if you turn it back, he can't be the normal Raees any more," he said.
MOH had said the boy was admitted to the children's intensive care unit in critical condition on June 22 and diagnosed with severe meningoencephalitis - inflammation of the brain and membranes covering the brain and spinal cord.
Mr Basharath recalled praying a lot during that time.
Doctors told him his son's case was very critical. He said he "did what a father had to do" and contacted different specialists and doctors for help.
An appeal for help for his son on social media network LinkedIn - where Mr Basharath uses the nickname Farath Shba - was shared more than 300 times.
Mr Basharath said he even contacted Foreign Minister Vivian Balakrishnan - who is an MP for Holland-Bukit Timah GRC - for help and the minister offered assistance despite being overseas at the time.
When contacted, Dr Balakrishnan said he would continue to support Mr Basharath's family and stay in close touch with them.
"We are all very sad. Mr Basharath has been a very devoted father and husband," he told ST via e-mail.
"He has gone through the ultimate nightmare of a parent."
The doctors said brain stem examinations showed that Zaheer Raees could not be revived, Mr Basharath said.
He spoke with a close family friend, who advised him to think things through before deciding how to proceed.
Mr Basharath said he had initially wanted to leave his son on life support for at least another month, citing cases where others had regained consciousness after being in long comas. But he said he could not bear the thought of his son's survival being dependent on tubes poking into his body.
"No parent should go through this," he said.
After the decision was made to pull the plug, Mr Basharath said he was allowed to say his final goodbye to his son.
"I held on to him until his heartbeat came to zero."
Zaheer Raees died on June 27, the day his older brother turned three.
Funeral prayers for the toddler were held at Maarof Mosque in Jurong West, and he was buried at Choa Chu Kang Muslim Cemetery on June 28.
MOH said on June 27 that the boy had no medical history of other conditions and was previously well.
"He was a healthy child," Mr Basharath added, citing the various developmental milestones the boy had achieved.
"He learnt how to speak, he learnt how to walk, he learnt how to run even earlier than his older brother," he noted.
Doctors told ST that cases like Zaheer Raees' were extremely rare.
Dr Yeo Tong Hong, senior consultant and head of neurology service at KKH, noted that while encephalitis has been reported as a complication of Covid-19 infection, such instances were very uncommon.
Asia Pacific Society of Clinical Microbiology and Infection president Paul Tambyah also said the chance of getting infected by three viruses simultaneously is very low. He suggested there could be a rare immunological problem that could have predisposed Zaheer Raees to complications.
Pointing out that both he and his wife had been vaccinated against Covid-19 and taken their booster shots, Mr Basharath advised parents to get themselves and their children vaccinated where possible.
They should also not hesitate to seek medical help should their children fall very sick, he said.
He and his wife are trying to be strong for Zayan's sake, as well as for their own sanity.
But he added: "I can't seem to accept the reality that he's moved on."
