His distraught parents now feel they have been dealt another blow because doctors have told them he will not be put back on life support if he needs it again.
William Burton was just a few months old when he was taken to Wellington Hospital in October 2013 with a fever and a red rash.
Five days and three visits later, he was finally diagnosed with E. coli meningitis and rushed to the Starship hospital in Auckland. But by then it was too late as the bacteria had already ravaged his brain.
Now, when Wendy and Derek Burton cradle their son in their arms, he doesn't return their smiles. Instead, his dark eyes mostly stare blankly and his body is limp.
Mrs Burton says she is still angry that her son was not diagnosed earlier.
The couple are considering taking legal action.
The Capital and Coast District Health Board has apologised "unreservedly" for the grief that has been caused and has brought in measures to try to prevent such a situation happening again.
The office of the Health and Disability Commissioner has investigated what happened and its report is due to be released today.
When William first became sick, his parents took him to the family doctor, a 24-hour medical centre and finally Wellington Hospital, where a senior paediatric house officer did not consult an on-call paediatrician.
Although hospital staff considered meningitis, they simply advised the Burtons to take William back to a doctor the next day if he was not better.
They did so and William was again taken to hospital. Rather than being examined in the emergency department, he was sent to the child ward, where another paediatric senior house officer diagnosed viral gastroenteritis.
The doctor consulted a senior colleague over the phone but that colleague wasn't brought in to physically examine the ailing child.
The Burtons didn't think the diagnosis was right because there didn't seem to be anything wrong with William's stomach. Reluctantly, they took him home.
Three days later, William was back in hospital. This time a lumbar puncture was performed and meningitis was immediately diagnosed. The Burtons were flown to the Starship and for the next month saw scans and pictures that showed William's brain dying.
"It's something you see very seldom, that extent of brain damage," Mr Burton said.
Mrs Burton said when they were told how badly disabled their son would be, she could barely stay standing.
Capital and Coast DHB says it has developed a formal assessment and discharge process for patients seen by junior doctors to ensure greater clinical oversight from senior physicians.
"Any child who re-presents to hospital within 72 hours is now assessed by a senior doctor before discharge," chief medical officer Geoff Robinson said.
"We have increased staffing to ensure a paediatric registrar, a doctor who has at least three years' experience, is on duty 24/7. All paediatric medical staff must also now complete a best-practice guideline on feverish illness in children under 5, from the UK's National Institute for Clinical Excellence."
The Burtons welcomed the changes, and hope they will avoid something similar happening to others.
Meanwhile, they and their 4-year-old daughter, Annabel, are left spending precious time with William, who is still in and out of hospital regularly and is there now.
Just last month, he spent a week in intensive care on a ventilator, arriving home days before his second birthday. Now the family have been dealt another blow, with both Wellington and Starship Hospitals saying they wouldn't again put William on life support if he needed it.
The consequences of this could be deadly for William, who is prone to serious respiratory illness.
"That's been really hard," Mr Burton said. "Wellington Hospital's been instrumental in how William is now, then on top of that they're not offering that extra support.
An Auckland DHB spokeswoman said out of respect for William's privacy, the board could not comment on the treatment options that might be considered should he be admitted to the Starship in the future. Wellington DHB would also not comment on the possibility of treatment in the future.
Mrs Burton said she was still angry, but her husband has eased a little.
"My anger used to be all consuming, now there's a little bit keeping me awake at night. There's more and more acceptance now," he said.
"There's a chance he could live for 20 years but there's a chance he could go with the next respiratory illness."
William spends a lot of his time in his special seats that support his body. His parents, who are helped by Mrs Burton's mother, Shunling Zhou, to care for William, have to keep opening his hands and feet to keep his limbs nimble.
William can swallow food and water and he's gaining strength in his neck. His legs and arms move, but not in a controlled manner.
Doctors say he's blind, but the Burtons think he can track movement sometimes.
"He likes to be cuddled and touched," his mother said.
William goes to respite care a couple of days a week and a special education kindergarten where the care workers train his brain to respond to its environment.
What is meningitis?
•Meningitis is the swelling of the lining around the brain and spinal cord. It can be caused by a virus, bacterium and other non-infectious causes.
•Bacterial meningitis can be caused by a number of different bacteria, including meningococcal, pneumococcal, haemophilus influenza type B (HIB), tuberculosis (TB) and group B streptococcal.
•Meningococcal meningitis can go on to cause septicaemia (blood poisoning).
•William's meningitis was caused by E. coli bacteria. Most cases of E. coli meningitis appear in new-borns and elderly.
