Stokes, the key witness, broke down in tears in the witness stand on the second day of the trial after being shown a graphic photograph of her son's bruised corpse for the first time.
She earlier told how Taylor had moved in with her in February 2015 when Ihaka was about 10 months old.
Stokes enjoyed an "amazing" relationship with Taylor who Ihaka called "Dad".
Taylor did much of the household chores, and despite the side-effects of his concussions, often tended to the "horrible sleeper" Ihaka in the night.
The Crown says that Taylor was suffering from sleep deprivation, headaches, and irritability caused by multiple concussions around the time Ihaka was developing an ear infection, when he allegedly caused the fatal injuries.
Just three hours after Ihaka died in hospital, Stokes was interviewed by police.
When asked if she had caused the fatal injuries, she replied: "I don't know."
She also alluded that she had a history of sleepwalking.
Again asked if she had anything to do with his injuries, she "laughed, not that I know of".
Shamy asked Stokes under cross-examination why she had said that if, as she claims now, she didn't do it.
She said that she had loved Taylor and didn't want him "to go down for this".
"That was me protecting him ... I knew what they were thinking," she said.
Later that night, when pressed further by police, she said: "I didn't do it."
Under cross-examination, Stokes who was 36 weeks pregnant at the time of Ihaka's death, denied losing her temper with the infant earlier on the day he died.
"Did you kill this boy?" Shamy asked her.
"No," she replied.
"I didn't hurt him. I don't hurt my children."
Shamy highlighted a series of what he described as "obsessive" text messages that Stokes sent to Taylor while he was out chopping wood two weeks before the death.
She bombarded Taylor with messages, asking him when he was coming home, to "please hurry up", and that she "can't get [Ihaka] to sleep".
Shamy suggested to her that she was not coping with Ihaka who she called a "grumpy, tired child".
But Stokes denied that, saying she was "just bored" and that she "doesn't like being alone".
Taylor is expected to give evidence later in the trial, and claim that after he came home from wood chopping, he found Ihaka "floppy", with raspy breathing.
A post-mortem found that Ihaka had suffered 59 separate injuries, including bruising to his forehead, around his eyes and ears, as well as his jaw line, skull, shoulder and arms.
He also had fractured forearms and shoulderblades, compression fractures in his back, and a brain haemorrhage.
Stokes says Taylor woke her later that night to say "something is wrong with Ihaka".
She found him lying on his back, "pale as, blue lips, and not breathing".
Stokes broke down crying in the witness stand as she described Ihaka not breathing, but taking "a big gasp" every "two to five minutes".
"I was just talking to Ihaka, telling him we would get through this."
Taylor, who was on ACC, also denies assaulting the child on July 2, 2015 - the day before the alleged murder.
The trial, before Justice Cameron Mander, continues tomorrow.
