In its charge sheet filed before Additional Sessions Judge Jasbir Singh Kundu, the agency said that sufficient oral, documentary and forensic evidence has come on record to substantiate that the 16-year-old accused had committed the murder on September 8 last year.
"It is, therefore, prayed that since a case of committing of murder of Prince on September 8, 2017 is made out against Bholu, this court may be pleased to take cognisance for the commission of offences punishable under 302 (murder) of Indian Penal Code against Bholu accordingly as per law," it said.
The victim's body was found with the throat slit in the washroom of the school.
The agency also gave a clean chit to school bus conductor Ashok Kumar, who was earlier arrested by the Gurgaon Police, and sought his discharge, saying there was no evidence to prove his involvement in the crime.
"He further stated that he had confessed to have committed the murder of Prince under coercion and threat of police officers concerned of Gurgaon police. He further stated that he was tortured and beaten by Gurgaon police officers," the agency said.
"During CBI investigation, no evidence has come on record to substantiate involvement of conductor Ashok Kumar in committing the murder of Prince in the ground floor washroom/toilet of the school or having attempted to commit sexual assault on the victim before committing murder.
"No blood stain was found on his cloths or his person before he had lifted the victim. Ashok Kumar's presence inside the washroom has been explained and found to be justified and true based on independent version of several witnesses and minute analysis of CCTV footages," the charge sheet said.
The court, which today rejected the bail plea of the accused, will consider the charge sheet on February 12.
The CBI took up the case from the Gurgaon police on September 22, following a nationwide uproar over the gruesome killing.
The final report also referred to the confessional statement of the accused where he had disclosed that he had used his mobile phone for making internet searches about poisoning, their effects and sources.
Subsequently after the incident on September 8, he had also made searches for removal and changing of finger prints on various websites, it said.
"The search of internet before and after the commission of murder for the above mentioned purpose thrown light on Bholu's conduct before the commission of crime, his intention to commit the crime and his conduct to escape from the clutches of law," the CBI said.
The agency said that the investigation revealed that Bholu was not good in studies and he had attempted to avoid mock examination in February 2016 by complaining that someone had mixed obnoxious substance in the water bottle because of which he was feeling drowsy.
"The documents collected from the Vidyalaya prove that he did not appear in the mock examination conducted in February 2016 and during the examination period, he was admitted in hospital for about three-four days.
"Academic records of Bholu were obtained from the the Vidyalaya in which he was studying. It was found that he was not good at studies and was below average in terms of academic performance," the agency said.
The CBI also quoted the statement of one of accused's close friend who had said that the accused was happy that a student of his school was murdered and the parent-teachers meeting was cancelled and that he would get 10-15 days' leave in the school.
The agency also claimed that the accused knew the victim very well prior to the incident and cited photographs collected from the school in which both were seen performing together in a function, which was corroborated by the school.
Earlier, the court had barred the media from using the name of the 16-year-old juvenile accused in the case and asked it to use fictitious names instead.
While the seven-year-old victim was named "Prince" by the court, the juvenile accused was named "Bholu" and the school was referred to as "Vidyalaya".
On January 8, the court had rejected the bail plea of the juvenile accused, imposed a cost of Rs 21,000 for "wasting the court's time" in baseless litigation and directed his father to deposit the amount.
The Juvenile Justice Board (JJB) had on December 20 last year held that the teenager would be tried as an adult and directed that he be produced before Gurgaon Sessions Court.
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