2003–2006: And The Story GoesAgnes Monica, TV series, and Whaddup

On 8 October 2003, Agnes released her first adult album, And the Story Goes, in which she worked with several famed Indonesian producers and songwriters, including Ahmad Dhani, Melly Goeslaw, and Titi DJ. The album production took a year and a half, including the audition process for the dancers  According to her record label, Aquarius Musikindo, the album sold 35,000 copies before its official release. It was later certified double platinum after selling more than 300,000 copies Four singles were released from the album: "Bilang Saja", "Indah", "Jera" and "Cinta Mati" (featuring Ahmad Dhani). The album received ten nominations at the 2004 Anugerah Musik Indonesia—the highest music awards in Indonesia. She won three awards for "Best Female Solo Pop Artist", "Best Dance/Techno Production Work", and "Best Pop Duo/Group" for her duet with Dhani. She also won "Best Female Newcomer Artist" at the 2004 Anugerah Planet Muzik in Singapore.

 In addition to promoting her debut album, Agnes also starred in several TV series during this time, playing the lead role in three: Cewekku Jutek, Bunga Perawan, and Cantik She won "Favorite Actress" at the 2003 Panasonic Awards and "Famous Actress" at 2004 SCTV AwardsAgnes launched her second studio album, Whaddup A.. '?!, on 10 December 2005. It featured five singles: "Bukan Milikmu Lagi", "Tanpa Kekasihku", "Tak Ada Logika", "Cinta Di Ujung Jalan", and "Tak Mungkin". In addition to working with Indonesian musicians, such as Melly Goeslaw, Andi Rianto, and Erwin Gutawa, she also collaborated with American singer-songwriter, Keith Martin.[6] Martin wrote two English songs for the album, including the duet "I'll Light a Candle". To promote the album, Agnes held a concert tour known as Clasnezenzation in four Indonesian cities: Bandar Lampung, Surabaya, Bandung, and Makassar.

 The album was commercially successful and she won two 2006 Anugerah Musik Indonesia for "Best Female Pop Artist" and "Best R&B Production".[20] She also won the "Most Favorite Female" award at the 2006 MTV Indonesia Awards. She was nominated for "Favorite Artist Indonesia" award at the 2005 MTV Asia Awards (beaten by Peterpan), but she grabs the youngest artist of all nominees in Asian category.[22] Selling more than 450,000 copies, the album was one of the top-selling albums of 2006 and was certified triple platinum
In 2005, Agnes appeared in the Taiwanese drama, The Hospital, co-starring with Jerry Yan, a member of the Taiwanese boyband, F4. She also appeared with Peter Ho in several episodes of the Taiwanese drama, Romance in the White House and starred in two Indonesian soap operas: Ku Tlah Jatuh Cinta and Pink, both televised on Indosiar. In 2006, she starred in the RCTI soap opera, Kawin Muda. She also decided to take a break from her study in Pelita Harapan University that year to focus on her entertainment career.