The tide turned when Ganguly took over in 2001. The first match(2003 World Cup) of Ganguly's era vs Pakistan showed what kind of cricket India wanted to play, aggressive & dominant cricket.
India won in Pakistan in 2004(test series & ODI series) & 2006(trashed Pakistan 4-1 in ODI series). India got hammered in the ODI series at home 2-4 in 2005, but went on to win the test & ODI series in 2007 at home. Pakistan also won the 2012-13 series 2-1.
Pakistan won the Asia Cup match in 2004, it was 1-1 in Asia Cup 2008, India beat Pakistan in 2010 Asia Cup. Kohli with 183 single handedly beat Pakistan in 2012 Asia Cup match. Afridi's sixes won Pakistan the 2014 Asia Cup match, India won both matches against Pakistan in 2018 Asia Cup, mauled Pakistan in 2023 Asia Cup. India have beaten Pakistan in 2003, 2011, 2015, 2019 & 2023 World Cup matches in this period.
Inspite of India winning in Pakistan in 2004, Pakistan beat Tendulkar less India in 2004 Champions Trophy & 2009 Champions Trophy, India beat Pakistan in 2013 Champions Trophy, 2017 Champions Trophy & 2025 Champions Trophy. Pakistan won the 2017 final, while India won in 2013 & 2025 finals.
T20Is have seen complete one side domination by India whether it's World T20 or Asia Cup. Pakistan are no match for India in T20Is, except for some time in 2021 when they beat an Indian team who played with safety first approach.