The court has heard how Taylor told police just minutes after the boy's death how he heard two "bangs" in the night and thought he'd fallen in his cot.
Taylor told the court he lied to police about the fall to protect Stokes.
He told the court that Ihaka was floppy and breathing raspily when he got into the child's cot earlier in the evening.
Worried that Stokes had done something, he baulked at getting medical help because he didn't want to get her into trouble.
He claimed he would've "gone to prison" for her if she'd admitted hurting Ihaka in a four-hour window that he was out of the house.
But Crown prosecutor Mark Zarifeh today said medical evidence heard in the trial - which Taylor dismissed, saying "science gets lots of things wrong" - completely undoes his story.
UK neuropathologist Professor Colin Smith believed it was a "maximum of minutes" from the time Ihaka received his injuries before he became unconscious.
Asked to comment on defence suggestions that Stokes inflicted the injuries in the afternoon - at least three hours before Taylor says he found him unresponsive in his cot - Smith replied: "That is not an explanation for the pathology that is present in this case."
Zarifeh said the medical evidence was not consistent with Taylor's account, and also independently showed that Stokes couldn't have inflicted the injuries on the Friday afternoon.
Taylor lied to police that fateful night, Zarifeh said, not to protect Stokes, "but to protect himself".
The Crown isn't saying that Taylor wasn't apparently an otherwise caring, loving father-figure, Zarifeh said.
But rather, it was a case that involved a "momentary snapping", in what was "a reckless killing... and in our law, that's murder".
Ihaka died in hospital from what is agreed was non-accidental, violent injuries, including broken bones and severe brain damage.
Defence counsel Phil Shamy reminded the jury, who have repeatedly seen disturbing images of Ihaka's bruised dead body from his post-mortem examination, to put aside any feelings of prejudice and sympathy.
"This young man is on trial for probably the most serious charge anyone can face - the murder of a child ," Shamy said in his closing address.
"This is a court of justice, not of emotion. You must be so careful in this trial."
Shamy accused police of "investigative bias" after Ihaka's death, claiming they had "made up their mind right at the beginning" that Taylor was responsible.
He said police appeared to have accepted almost immediately what Stokes told them, yet they pushed Taylor to confess.
On the night Ihaka died, Stokes was asked by police if she had harmed him.
She replied, "I don't know", adding that she had a history of sleepwalking.
Later, when police pressed her further she denied any involvement in his death.
During the trial, she again repeatedly denied inflicting his injuries.
Shamy told the jury that the onus was on the Crown to prove beyond reasonable doubt who killed Ihaka.
"Mr Taylor proves nothing... you've got to be sure. Sure it wasn't Mikala Stokes and sure it was him," Shamy said.
"If you're not sure, you've got to give Mr Taylor the benefit of the doubt.
"You cannot convict Mr Taylor by default, just because he's the only one sitting here."
Taylor also denies assaulting the child on July 2, 2015 - the day before the alleged murder - although he yesterday admitted dropping him during a dizzy spell.
The trial continues tomorrow morning with Justice Cameron Mander summing up the evidence for the jury before it retires to begin deliberations.
