Working in the science department, she became Editor of the BBC One series "QED", and then executive producer of the documentary series "Animal Hospital" and "The Human Body". Heggessey was considering leaving the BBC again and returning to working in the independent sector, when she was offered the position of Head of Children's BBC. As her daughters were at the time aged four and eight, she decided to accept the role, later explaining that "Short of taking over Hamleys, this was the next best job for them." She took up this post in 1997. It was as Head of Children's BBC that she became involved in the dismissal of "Blue Peter" presenter Richard Bacon. In October 1998, the "News of the World" newspaper revealed that Bacon had taken cocaine, and he was subsequently sacked from his job as a presenter on the high-profile children's programme. Heggessey appeared on-screen in a specially-recorded one-minute address to viewers shown directly before the first episode of "Blue Peter" to be screened following Bacon's sacking, on 19 October 1998, to explain to young viewers why Bacon had been dismissed, stating that he had "not only let himself and the team on "Blue Peter" down, but he has also let all of you down badly." In 1999 she was promoted to Director of Programmes and Deputy Chief Executive of the BBC's in-house production arm, BBC Production, responsible for supervising in-house output across all the various genres. She was in this role for little over a year however before she was promoted to Controller of BBC One, a post she took up on 1 November 2000. In this position she was responsible for co-commissioning the channel's output with the various heads of department — drama, news, etc. — and deciding the channel's overall strategy and schedule. She had previously been sounded out about the job in 1997, after Michael Jackson's departure, but had turned down the opportunity as she felt she was then not yet experienced enough. During Heggessey's five years in charge, BBC One's audience share fell by 19.9%, to 23%, although this was in the context of declining audience figures across all British television channels due to increased competition from multichannel digital television. However, in 2001 BBC One overtook its main rival ITV1 in terms of annual audience share for the first time since the rival channel had launched in 1955, although much of this was down to the success of the channel's daytime television line-up, which had its own Controller in Jane Lush.