In 1998, Allan Young shook five-week-old Michael Winn at the home he shared with his girlfriend in north west London, leaving his son severely disabled with only a 65% chance of surviving to the age of 11, a court heard.
The following year, Young, now 36, admitted causing grievous bodily harm but when the child died in 2011, he was further charged with manslaughter.
Michael's death was a direct result of the injuries he suffered years earlier which caused cerebral palsy and curvature of the spine, the Old Bailey heard.
His physical and intellectual development was impaired to such an extent he had trouble breathing, was blind, incontinent and could not speak, jurors were told.
At the time of his death, his adoptive mother described him as having the functioning age of six weeks, the court heard.
Prosecutor Zoey Johnson QC told jurors that Young did not mean to cause his son really serious harm but the evidence would show he was nevertheless responsible for Michael's death.
Young, of Glasgow Road, Wishaw, in north Lanarkshire in Scotland, denies manslaughter.
Young was living his partner Erica Francis in Belsize Road, north west London, when he shook their newborn baby on the morning of April 16 1998, the court heard.
When Ms Francis, then 17, woke up later that day, she noticed Michael had become "all floppy" and had "staring eyes that did not focus", Ms Johnson said.
At first she thought Michael had caught flu from her, but the next day he was still sick.
The lawyer said: "Erica described seeing Michael lying in his crib awake but lifeless. When she picked him up, he just slumped in her arms."
She decided to call the health visitor, but before she could, Young admitted he "may have hurt Michael" and shaken him because he would not stop crying, the court heard.
When the baby arrived at the Royal Free Hospital in London, he was "pale and fitting". A CT scan revealed he had suffered bleeding on his brain and he was diagnosed with "shaken baby syndrome", the prosecution said.
He was eventually discharged from hospital in May 1998 into the care of Camden social services, which placed him with foster parents before he was adopted.
Meanwhile, both parents were arrested and Young was charged with inflicting grievous bodily harm.
At the time, Ms Johnson said: "Michael was still very much alive although severely disabled and, following the assault by this defendant, Michael was left with severe brain damage."
On January 11 2011, his adoptive mother Karen Heppleston-Winn noticed Michael's breathing had stopped and despite the efforts of medics, he died in the night on January 23 2011 at the age of 12.
A post-mortem examination found he died of "respiratory insufficiency caused by pneumonia and the marked curvature of the spine" as a result of the injuries Michael suffered as a very young infant, Ms Johnson said.
She added: "There was a cause and effect role between the head injury sustained while Michael was a baby and his death at the age of 12."
There was no evidence of a natural disease which could account for the injuries and no evidence of any recent brain damage.
Young was arrested in Scotland in March 2011 and told police in interview that he had "accidentally shaken" Michael for mere seconds after he had been up all night.
At the time, he said he and Ms Francis had been having problems in their relationship and they were trying to sort things out, the jury was told.
Ms Johnson told the jury: "Up until April 16 1998, we suggest that Michael was developing normally but at 11am in the morning of April 16, when Erica Francis picked Michael up from his crib, it was obvious that Michael was very unwell and the evidence suggests that by this time Michael had already suffered the injury to the brain that caused his cerebral palsy and eventually his death.
"This defendant has admitted shaking Michael earlier that morning. Whether the defendant has admitted all he did to his son is a matter you will have to consider."
The trial continues.