During promotion for the single, Katona announced her pregnancy and subsequent decision to leave the group.
Following the commercial underperformance of both "Follow Me" and the initial release of the album, Atomic Kitten persuaded their label to release "Whole Again" as a last-ditch attempt to keep their record deal. While Innocent Records planned to release "Whole Again" as Atomic Kitten's fourth single at times, it was eventually replaced by " Follow Me" to lead the UK release of parent album Right Now. While Innocent Records liked their version, they asked Godfrey and Padley to re-record McClarnon and Hamilton's vocals at least two more times, though they eventually decided on using the original vocals that had been recorded in West Hampstead in the end. Padley and singer friend Angie Giles also provided vocals for the gospel part near the end of the song for which the producers tracked about forty vocals and put several delays and effects on it to sound like a choir. While the duo kept much of the "underwater organ sound" from the original session, they were forced to replay other elements and added a couple of additional loops from the sample albums Vinylistics 3 and Advanced Orchestra to the track. As well as recording the new vocals, Godfrey and Padley also took over the job of producing "Whole Again," although they were careful to preserve the features of McCluskey and Kershaw's original version, including Katona's spoken bit in the middle. A hasty affair due to the band's hectic schedule at that time, much of the vocals were recorded within 30 minutes, with McClarnon and Hamilton each singing the whole song twice only. Recording of the new verses took place at Godfrey and Padley's West Hampstead music studio. We very carefully worked out what the vocal range of the Kittens was, because the last thing we wanted was to write a melody that was fantastic but that they wouldn't be able to sing." Godfrey later described the process as "quite difficult, because the chorus of the song was so hooky that the verse had to lead up to it but not overshadow it, which is why it ended up sounding as low as it does. With the chorus being already there, Godfrey and Padley decided on writing a melody for the verses and changed most of the chords in "Whole Again," but were not able to change its key. While this version was included on the Japanese version of Atomic Kitten's debut album Right Now (2000), Innocent Records A&R manager Hugh Goldsmith felt that it was still a half‑finished song and asked songwriters and producers Jem Godfrey and Bill Padley to re-write it for the UK version of the album. A mid-tempo ballad that combines a strolling beat and one-note string crescendos, it initially featured all lines spoken by Kerry Katona with only the chorus sung by Liz McClarnon and Natasha Hamilton. "Whole Again" was written and produced by Orchestral Manoeuvres in the Dark members and Atomic Kitten founders Andy McCluskey and Stuart Kershaw.