The duo, who returned to the JNU campus last Sunday after having gone missing since February 12, drove from the administrative bloc to the main gate of the university, got into a Delhi Police vehicle and were taken to an undisclosed destination.
Police sources said Khalid and Bhattacharya surrendered at around midnight.
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Khalid and Bhattacharya are likely to be produced before a magistrate today.
Khalid and Bhattacharya are among the five students who, along with JNUSU President Kanhaiya Kumar, had allegedly shouted anti-national slogans at an event organized in the university campus to mark the death anniversary of parliament attack convict Afzal Guru on February 9.
Besides Kumar, Khalid and Bhattacharya, the other students are Rama Naga, Ashutosh Kumar and Anant Prakash.
Delhi Police had issued a look-out notice on February 20 against Khalid, Bhattacharya, Naga, Ashutosh and Prakash.
Earlier, Khalid and Bhattacharya left the JNU campus at around 1150 pm tonight for the surrender.
The university students formed a human chain to prevent the media from following Khalid and Bhattacharya when they were leaving the campus this evening. Earlier in the day, Delhi High Court Justice Pratibha
Rani said she will tomorrow hear the plea of Khalid and Bhattacharya seeking protection during their surrender to the police.
However, the High Court refrained from giving any specific direction on granting any interim protection from their arrest, with Justice Pratibha Rani saying "let the matter be heard tomorrow."
Advocate Kamini Jaiswal, appearing for Khalid and Bhattacharya, sought protection from their arrest till tomorrow but the judge said "I am simply re-notifying the matter for tomorrow. We are not disposing of the petition. Let it be heard tomorrow."
While refusing to grant protection from arrest, the court asked both petitioners to secretly give details of the date, place and time where they will surrender, to the court and senior police officials will ensure their safety.
DCP (South) Prem Nath, however, did not agree to the place the petitioners wished to surrender, saying he has some inputs due to which the place mentioned by the accused was not accessible to police.
At this, the judge called the DCP and the accused's counsel Trideep Pias to come to her chamber and give reasons for the objection.
After nearly 10 minutes of in-chamber discussion, the judge posted the matter for tomorrow for further consideration.
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