It heard final submissions on Thursday before closing its hearing into the school and the abuse inflicted on boys, by brothers in the Order of St John of God, between 1955 and 1984.
More than 30 witnesses have given evidence over the last seven days - many survivors, some experts and some senior members of the Catholic Church.
Through its lawyer, Sally McKechnie, the Church again apologised for what happened.
''This harm should never have happened and it is a great shame and deep regret to the Church that it has.''
She acknowledged the courage of survivors who had shared their experiences.
''The brothers and the Church have heard their pain, and they have heard the anger, and frustrations.
''That Marylands was a place of sexual, physical and psychological abuse was horrific and the Church apologises to you, survivors, to your families, whānau and to the hundreds of co-workers who worked in these institutions.''
SNAP, the Survivors Network for those Abused by Priests said the evidence, harrowing as it was, really just confirmed what everyone already knows.
''The abuse was made because it was perpetrated by Catholic religious priests and brothers who vowed to care for vulnerable children,'' said spokesperson Dr Christopher Longhurst.
Dr Longhurst told the inquiry the Church used its power to silence victims and evade responsibility.
''We heard over and over again how survivors tried to report the abuse they suffered but were disbelieved on one hand and discredited and silenced on the other hand.
''Where was there shame decades ago when child victims and their parents first reported the abuse? Where was their shame when disgraced brothers were shipped overseas instead of facing justice? Where was their shame when some of their victims took their own lives?''
Dr Murray Heasley is from another survivor group, the Network of Survivors of Abuse in faith-based institutions.
He described Marylands as yet another example of prolific abuse that has happened in an institution, that was known about.
''Neither the Church or the State took any action. It operated at a time when abuse happened largely in bricks and mortar institutions where it could easily be hidden or covered up by invested officials to protect their own and their institution from accountability.''
Liz Tonks, also from the network, is in no doubt about the extent of abuse, both in the past, but also the present.
''New Zealand tolerates abuse of its children and unless we change as a society it will not stop. Unless we dismantle the system that supports it, it will not stop. Unless we change our culture of acceptance in New Zealand, it will not stop.''
For Tonks, what happened at Marylands needed to be labelled exactly what it was.
''Marylands was in reality a state-supported, church run brothel, that serviced the needs of paedophiles and the children were essentially sex-slaves and labourers, funded by parents and taxpayers.''
Clinical psychologist and nun, Dr Michelle Mulvihill used to work for St John of God, but is now one of its harshest critics.
She described the apologies coming from the Church as a sham.
''It's evidenced by the impassive charade that you have witnessed over the past days of this inquiry by the apologists who have appeared here. It is also evidenced by the absence at this Commission of those key brothers who were in charge of things in the 1970s and 1980s and who are still alive today.''
Mulvihill said when the St John of God Order came to Marylands in 1954, the Catholic Church in New Zealand engaged a group of untrained religious strangers to educate children in need of care.
''These men then used and abused their power, destroyed the lives of children and then discarded them.''
She ended with a message directly to survivors.
''Continue to demand that your needs are met later in life because they were never met when you were a child. Do not be afraid to speak. Be very afraid of what will happen to the whole of this most uncomfortable truth, if you do not.''
The Catholic Church's lawyer, Sally McKechnie, told the hearing that it was understandable from the evidence that the harm to survivors has caused them to lose their faith in institutions, such as the Church.
''The destruction of that faith then extends to other institutions, such as concerns that the police are being controlled by the Catholic Church, and it impacts on society and the Church's efforts to improve, and this is a real challenge.''
The final word went to Commission chair, Coral Shaw, who assured survivors that they have been listened to.
''This is not just in the past, but the pain, both personal and social consequences which flow from them for the survivors, rests with all of us. It lives on and I implore those who have listened, to have heard, who have felt and understand, to support all calls for action.''
Judge Shaw said the Commission will eventually report back with recommendations to satisfy survivors, so that the abuse will never happen again and those responsible for it and the institutions, will be made fully accountable.