Michelle Dearing had left her baby Chayse alone with her new boyfriend Dwayne Lindsey in June 2016, but came home to an "emotional, chaotic scene" at their temporary lodgings at Glenroy.

Lindsey, who has denied he intended to kill the six-month-old boy, is on trial in the Supreme Court of Victoria for murder.

The court was told on Friday the baby had severe traumatic brain and spinal cord injuries, marks on his neck, bruising and abrasions on his groin and retinal bleeding.

Prosecutor Nicholas Papas QC said Lindsey, 34 at the time, claimed he fell asleep with the child on his chest, then woke and jumped when he thought a spider was crawling on him.

He claimed the baby rolled off his chest and hit his head against a wall heater.

But Mr Papas said Lindsey's explanation was incongruent with medical reports, which showed Chayse's death from a head injury was unlikely to have been accidental.

Ms Dearing and two of her friends had gone to Kmart after 4am.

At 8.21am, she got a call from Lindsey saying something was wrong with Chayse, that he wasn't breathing and that he had blood coming from his nose.

"It was an emotional, chaotic scene when Ms Deary and the others got back," Mr Papas said.

"She (Ms Deary) was overcome with emotion and collapsed."

Ms Deary noted Chayse had been changed from his blue Ralph Lauren onesie into a white fluffy onesie with bear ears on the hood, Mr Papas said.

It is also alleged Lindsey later told a witness he had, in fact, struck and kicked the baby.

Defence barrister Scott Johns said Lindsey did not intend to kill the child.

"Whatever you think of Dwayne Lindsey, he's not a murderer," he said.

"None of his actions came from an intention to cause any harm at all."

Lindsey's trial is expected to run for a week.

Australian Associated Press