The only person who was looking after a five-month-old baby the day he died in Alice Springs has said he was not aware of how the infant came to be covered in bruises.

On the final day of the coronial inquest into the death of Michael Smedley, Oliver Deighton gave evidence.

Michael's mother Tayla Smedley had entrusted her son in the hands of Tamara Cole, who left the baby on the day that he died with her then boyfriend, Mr Deighton, a disability carer.

Yesterday the inquest heard that when he died in July 2012, Michael had 26 bruises over both bone and soft tissue, was suffering from three major pointers to shaken baby syndrome, and had damage to his anus and blood on his nappy.

It was also initially thought that seven sperm heads were identified from a swab taken inside the anal cavity, although later investigations could not identify any.

Deighton 'unaware of how bruises occurred'

Mr Deighton agreed he was the only person looking after Michael the morning he died and that he was alone with him in the hours leading up to the boy becoming unconscious.

But when asked if he knew how the bruises occurred he said: "I'm not aware of how the bruises occurred, they could've taken up to 18 hours to form.

"It could have happened from the night before."

Oliver Deighton said he did not know how Michael Smedley came to be bruised. ( Supplied: Facebook )

A doctor who gave evidence testified that bruises of the type Michael had would have formed much more quickly, possibly within three minutes.

Ms Cole also gave evidence today.

She bowed her head and appeared visibly upset as counsel assisting the coroner Kelvin Currie asked her about the size, shape and colour of the 26 bruises left on Michael's body.

"I only remember one bruise," she said. "On his back, the rest I can't explain but they weren't there when I left for work."

Ms Cole said she was running late the day Michael died, and had to leave him in the care of Mr Deighton.

She said while she was at work a friend came by to collect some keys off Mr Deighton but loud music prevented him from hearing the door.

Later that morning Ms Cole returned to collect Michael and take him to day care, but when she arrived she said he had been put down in his nursery to sleep, which she said was an unusually early time for his mid-morning nap.

After going to the toilet she said she heard a loud scream from the nursery, and said she knew something was wrong.

Michael Smedley 'looked like a rag doll'

When she walked into the hall Mr Deighton was holding baby Michael. "He looked like a rag doll, I was frightened," she said.

"I immediately took him and put him on the kitchen bench and started performed CPR then called an ambulance."

Michael was rushed to hospital and it was there that doctors noticed the extensive bruises and abrasions on the five-month-old.

Michael Smedley had indicators for shaken baby syndrome when he died, the inquest heard. ( Supplied: Facebook )

In her witness statement, Ms Cole said a day after Michael died she said to Mr Deighton: "Just tell me what happened and I'll protect you."

It was then that he told her Michael sustained the horrific injuries after falling off a baby change table, but Mr Deighton said he caught the baby just in time.

Forensic Scientist Denise Grover also gave evidence today and said the anal swab taken from Michael did not have enough material to draw a forensic connection to anyone, but that the slide contained sperm.

"There were seven spermatazoa on the slide," she said.