In the charge sheet, the agency said that prime accused in the high profile murder case, Indrani Mukerjea, was not happy with the love affair of Rahul and Sheena.
It also states that Rahul met Sheena at Peter's house and their friendship grew into love. In 2008, Sheena told Rahul that she was in fact Indrani's daughter.
Indrani who did not approve the love affair quarreled with Sheena and sent her to Guwahati and later, Delhi. When Sheena fell ill in Delhi, Indrani called her daughter's former boyfriend, Kaustubh Saikia, and asked him to take her to Bengaluru.
Rahul came to know of this and visited her in Bengaluru and found that the medicines given by Indrani to Sheena were sedatives meant for mental illness, according to the charge sheet.
Describing the plot and the purpose behind the murder, the CBI in their charge sheet, added, "Indrani had entered into a criminal conspiracy with the co-accused namely Sanjeev Khanna, Shyamwar Pintu Rai for abduction and killing of Sheena Bora and Mekhail Bora."
"In pursuance of the said criminal conspiracy, Indrani along with Shyamwar and Sanjeev abducted Sheena on 24/4/2012 along with the co-accused persons and killed her in a car by administering sedatives and strangulating her and thereafter disposed her body on 25/04/2012 at Gagode Khind, Khapoli-Pen Road, Raigad by burning it. Indrani also attempted to kill Mekhail."
The investigating agency is also probing allegations that a financial dispute was at the heart of the case, especially a transaction that involved Rs 1,300 crore.
The CBI alleged in court that Indrani and Peter hatched the murder plot in early 2012. Indrani returned to India on April 23, 2012 while Peter stayed back in the United Kingdom and returned on April 26, a day after the murder, the CBI stated.
On his return, Peter and Indrani maintained that Sheena had moved to the US whenever they were confronted by Rahul, the CBI said.
"Indrani had purchased a flat for Sheena in Delhi through a gift deed but she later terminated it after learning about Sheena's affair with Rahul. Sheena then allegedly started blackmailing Indrani, threatening to expose her before her social circuit as she had a birth certificate which proved that Indrani was her mother and not sister. Sheena demanded a three bedroom flat in Mumbai from Indrani.
This appeared to have irked Indrani, who then hatched a plan to kill Sheena along with (her former husband) Sanjeev Khanna. Peter played an active and crucial role in the case," stated the 1,000-page CBI charge sheet.
On Friday, the judicial custody of Indrani, her ex-husband and her driver Shyamvar Rai -- was extended on Friday till December 3 to allow investigators to continue with their probe.
The agency also charged the founder of the NewsX television channel and group, Peter Mukherjea, with murder and criminal conspiracy in connection with the murder case.
The CBI said that while it had earlier booked Peter Mukherjea under several sections of the Indian Penal Code, he had also been additionally charged under Sections 302 and 364, and would be prosecuted accordingly. It said that four serious charges have been levelled against him.
On November 3, the judicial custody of Indrani, and the remaining two accused was extended till November 7 after their earlier remand had ended.
Earlier, this month, the CBI was given permission by the Bombay high court to question all the three accused in the Sheena Bora murder case.
Sheena Bora constantly 'blackmailed' Indrani: CBI
Peter Mukerjea charged with murder; CBI claims Sheena killed for property
Peter Mukerjea arrested, taken to court: Latest in Sheena murder case
Sheena case: CBI arrests Peter Mukerjea