During the 30-year conflict known as the Troubles, Ardoyne had become segregated – Ulster Protestants and Irish Catholics lived in separate areas.

Some protesters shouted sectarian abuse and threw stones, bricks, fireworks, blast bombs and urine-filled balloons at the schoolchildren, their parents and the RUC.

The "scenes of frightened Catholic schoolgirls running a gauntlet of abuse from loyalist protesters as they walked to school captured world headlines".

[1] Death threats were made against the parents and school staff by the Red Hand Defenders, a loyalist paramilitary group.

[citation needed] In December 2000, Protestant taxi driver Trevor Kell was shot dead in Ardoyne.

[4] The next day, loyalists retaliated by shooting dead Catholic man Gary Moore as he was renovating a house in Newtownabbey.

[5] On 19 June, a fight broke out between men putting up loyalist paramilitary flags and the occupants of a passing car.

[1][7][8][9] In the summer of 2001, the RUC received intelligence that UDA members were planning to "exploit community tensions" to kill Irish nationalists, Catholics and/or police officers.

[9] On Tuesday 19 June, Royal Ulster Constabulary (RUC) officers had to protect children and parents entering the school after they were attacked by loyalist stone throwers.

Following the incident, a blockade of the school developed, with loyalists standing across the road and RUC officers keeping the children and their parents away.

On 20 August, a 'paint bomb' was thrown at the home of a Protestant man in Hesketh Park, smashing a window and causing paint damage to furniture.

[15] Later in the day the Red Hand Defenders (RHD), an illegal loyalist paramilitary group, warned parents and children to stay away from the Ardoyne Road.

The blast caused an oil tank to catch fire and the flames spread to three houses, one of which was completely destroyed.

For months after the protest ended, police and British Army armoured vehicles sat outside the school and at the junction of Alliance Avenue each day.

In the morning, six loyalists, one with a gun, rampaged through the grounds of Our Lady of Mercy Catholic girls' secondary school, smashing 18 cars with crowbars.

In the afternoon, Protestant pupils from Boys' Model Secondary School were ferried home in police armoured Land Rovers past nationalist crowds on Crumlin Road.

On Monday, more than 750 armed police officers and soldiers were sent to guard Catholic schools in north Belfast while armoured vehicles lined Ardoyne Road.

[21] In February 2002, Holy Cross schoolchildren travelled to County Galway for a free holiday as guests of Peacock's Hotel.

PUP politician Billy Hutchinson said "The protest was a disaster in terms of putting their cause forward but it was a genuine expression of their anger and frustration and fear over what is happening in that part of North Belfast".

[1] A month before the protest was ended the Department of Social Development announced a housing redevelopment package for Glenbryn.

Ardoyne Sinn Féin councillor Margaret McClenaghan says the common perception was that loyalists were being rewarded for intimidating schoolgirls.

It is actually a strategy of social political engineering between the NlO and the Housing Executive, to solve the issue of interface tension".

The North Belfast Community Action Unit was set up to foster inter-community talks, focusing on social and economic issues of interest to Ardoyne and Glenbryn.

[1] In December 2024 papers declassified under the thirty-year rule revealed that the government of the Republic of Ireland had offered him the use of a flat leased by the Department of Foreign Affairs in Belfast after he received death threats.

[25] He declined the offer as he didn't want to leave Ardoyne and feared that drawing publicity to the threats would have an adverse effect on the children.

When Holy Cross teachers asked girls in Primary 6 (aged 9–10) to draw a picture many had drawn mothers and fathers crying, surrounded by people with angry faces.

[27][28] Fr Aidan Troy, head of the board of governors of the school, expressed concern that the drama could reignite the problem.

On 25 April the Police Service of Northern Ireland (PSNI) were called to the school to disperse a loyalist protest being held outside it.

The protest was sparked by false rumours on social networks that Belfast City Council employees were due to arrive to remove the flags and the paint.

[30] In the early hours of Sunday 23 April 2017, a bomb was found by a police patrol outside the gates of Holy Cross Boys' Primary School in Ardoyne.