Joshua Jones, was found dead at the home of Nichola Bowman and Wayne Davenport in Tilbury Place, Runcorn, Cheshire, on November 6 2007.
The two-year-old had sustained a bang to the head and died from brain swelling.
In hospital, medics discovered a variety of bruises and marks on his tiny body - including teeth marks matching Davenport's dentures.
Almost two weeks before he was killed, Joshua was taken to hospital with a double break to his left arm.
He also had two bruises to his penis, three bruises to his thighs, three to his knees and bruises to his back and arm.
Unbeknown to doctors at Warrington General Hospital he also had two fractured ribs which did not show up on an x-ray.
Today, Chester Crown Court heard Bowman, 24, blamed the broken arm on her mother Michelle Littlemore's partner John Deane - who lived close by in Runcorn.
Michael Chambers QC, prosecuting, said: "When Joshua was admitted to hospital on Friday October 26 2007 'alarm bells rang' with doctors, social workers and police officers who attended.
"In this case there were all the signs typical of systematic child abuse.
"For that reason rather than be sent home after his left arm was put in a plaster cast as would usually be the case, Joshua was admitted to a paediatric ward at Warrington General Hospital.
"This was to enable him to be examined further and for the case to be investigated.
"On the following Thursday afternoon Joshua was discharged from hospital and allowed to go home with his mother rather than be admitted into the temporary care of social services.
"The doctors, social workers and the police involved had held a number of meetings.
"Joshua's family was not previously known to social services.
"They accepted at face value the explanations they were given.
"That clearly was the wrong decision."
He added: "However, the prosecution do say that those who made that decision were to some extent deceived by the actions of Nichola Bowman and her family.
"Firstly, Nichola Bowman and her family explained away the fracture to the arm by saying that it must have happened when Michelle Littlemore's partner John Deane had lifted the child up on the previous Wednesday, October 24."
Mr Deane said he had thrown Joshua into the air by his hands and caught him round the waist.
He later told police he only said that so "as a family we could get Joshua out of hospital".
Weeks earlier, Joshua's biological father, Jason Jones, had seen two black eyes on his son.
And on October 31, while Joshua was in hospital, Bowman sent Mr Jones a message reading: "Let me no wen social services have bin.
"r u hoin c mention his black eyes coz if you do they mite not let him home. i NOT told them u take coke."
Mr Chambers said: "This could be construed as a threat: 'I won't mention you take cocaine if you don't mention the black eyes'."
He added: "So when Nichola Bowman took Joshua home she knew perfectly well what had been happening to him at the hands of the defendant Wayne Davenport - or at the very least ought to have known, yet did nothing to protect him.
"On any view, the authorities at the hospital made it abundantly clear to her that they viewed all these injuries as highly suspicious.
"She should have ended the relationship there and then.
"She certainly should not have allowed Davenport to be alone in the house with Joshua upstairs asleep when she knew of the likely risk that Joshua would wake up and call for her, with the likelihood that Davenport would enter the bedroom tired, under the influence of cannabis and likely to lose his temper."
Davenport was alone in the house with Joshua when he died.
He denies manslaughter and an alternative charge of causing or allowing the boy's death.
Bowman faces one count of causing or allowing Joshua's death - which she denies.
The seven women and five men of the jury have heard that Joshua was frightened of Davenport - who moved into the house two weeks after meeting Bowman - and did not like being in the same room as him.
