The rampant abuse got attention courtesy an audit of the Tata Institute of Social Sciences (TISS).
Terming the case horrible, SC wondered in October 2018 what was happening in India.
CBI didn't find evidence of inmates being murdered
Last year, the premier investigating agency told the top court that Thakur, in collusion with his aides, could have murdered 11 girls.
But today, CBI went back on its allegations. Attorney general KK Venugopal, appearing for the agency, said the girls (believed to have died) have been traced.
And the two skeletons, that were dug out from compound, belonged to a woman and man.
Separately, CBI investigated 17 shelter homes, found 13 guilty
Further, Venugopal informed the court that CBI investigated 17 shelter homes and filed charge-sheets against 13. The rest of them weren't found guilty of any wrong-doings.
In fact, CBI also told the court that it has asked Nitish Kumar-led government to take action against these NGOs, like canceling their registrations.
A bench, headed by Chief Justice of India, SA Bobde accepted CBI's status report.
IAS officers among officials facing action
As it turns out, CBI has also urged Kumar to initiate action against officials, who turned a blind eye towards wicked NGOs and allowed them to continue their devious deeds. Of the 70 officials facing action, 25 are IAS officers.
The Muzaffarpur episode demolished myth of "perfect" governance in Bihar
The shelter home episode raised questions on Kumar's "spotless" image, especially since a minister of his government was found to be a friend of Thakur.
Chandrashekhar Verma, the husband of Bihar's former social welfare minister Manju Verma, was Thakur's "close friend".
Later, Verma resigned from the ministerial post but only after massive hue and cry. And as expected, she has claimed innocence.