The promising youngster had taken the Premier League by storm after his dream debut goal against Arsenal as a 16-year-old, and the Toffees were thereafter resigned to losing their prized asset.
Manchester United and oil-rich title contenders Chelsea were vying for his signature, with Jose Mourinho attempting to lure Rooney to Stamford Bridge and help him win his first title in English football.
However, it was Sir Alex Ferguson who managed to convince the wonderkid to travel a short distance from his hometown to Liverpool and sign in a £27 million deal. It was a signal of intent from the Red Devils and, for the first time as Chelsea owner, Roman Abramovich had missed out on his main target.
Nine years later, the opportunity arose once again to sign Rooney, with both Mourinho and Abramovich keen not to be beaten again. In essence, they were determined to stop at nothing to sign him, with two bids rejected in the summer, per BBC Sport.
But this time around, there was more than just the one reason for their pursuit of the Merseyside-born forward.
Hailed as one of the best players of his generation, it's been a pleasure to witness the rise of Rooney from an ill-tempered teenager to a well-groomed, world-class striker. Granted, he is not yet a finished article, and there are always going to be doubts about his fitness going into the latter years of his career.
However, his quality is simply undeniable, and to say he is the best player England has produced this side of the Millennium is not as bold as it may appear. So for Chelsea to be interested in signing Rooney is not really much of a surprise.
As we have all discovered, if a club wants to buy English talent, they are forced to pay a premium price for that player. A prime example is the £35 million Liverpool paid for Newcastle striker Andy Carroll, who then moved to West Ham for £15 million.
In that sense, the reported £40 million requested for Rooney does not seem such a bad valuation, considering there is an obvious gap in quality between the two.
Of course, Chelsea decided to give up on Rooney for the time being and sign Samuel Eto'o on a free transfer for Anzhi Makhachkala. It covers them in the short-term, with Romelu Lukaku joining Everton on loan for the season, but expect them to be back in for Rooney should the chance come about once again.
Chelsea had lacked a focal point of their team for some time. In fact, only after Didier Drogba's transfer to Shanghai Shenhua did it become apparent how much the Blues needed a target man.
Of course, many would say that with £50 million striker Fernando Torres spearheading the attack, the Spaniard should be able to fill the gap left by veteran striker Drogba. But despite netting 23 goals last season, the West London side lacked a technical player who could link the play between the midfield and attack.
Sure enough, Juan Mata is the man who would be deployed in this role due to his influence in the playmaker role. But the comparisons between the little magician and Rooney stop at the fact they have the same shirt number.
Mata would float around the pockets of space in between the opposition defence and midfield, looking for opportunities to slide in his teammates, but essentially he couldn't play as a 'false nine' because, with a small and slight frame, he is unable to hold up the ball and bring others into the play.
Rooney, on the other hand, is superb at doing this.
Whether it's dropping deep to bring the ball forward, or receiving a pass into feet, the 27-year-old is more than capable of leading the line, and would have been ideal addition to Chelsea's star-studded attacking options.
Torres may be able to score goals, but as an out and out striker, that's his only real responsibility. With Rooney, it's a bit more complex.
Undoubtedly, he is more of a complete player than Torres or Mata, and it's that versatility which made him such a lucrative option for Chelsea and more importantly, Mourinho.
His tendency to float out to the wings and drop into deeper areas of midfield encouraged Sir Alex Ferguson to utilise him there before retiring, and it's realistic to think Mourinho would want to use him there too if required.
For most managers, the main objective is to win games on the pitch. For Mourinho, the idea of trying to gather as much momentum before a game is crucial in determining the match result, and thus, we discover the use of his famed mind games.
As we saw on Transfer Deadline Day, Arsenal's signing of Mesut Ozil meant they were also looking for a striker for him to link up with, and a made a loan move for Chelsea striker Demba Ba per John Drayton of the Daily Mail.
Originally keen on the idea of Ba leaving after Samuel Eto'o's arrival, Mourinho waited until the last moment before closing the door on an exit. Asked to explain his move, the Portuguese tactician replied: "I did not accept Arsenal's offer for Demba Ba because added to their signing of Ozil, they would have been title contenders", per ESPN.
Interestingly, it's that obsession with being weakened which left Mourinho with the idea that delaying his decision on Ba before rejecting it would inevitably give Arsenal no time to sign another striker, and thus Chelsea gained from Arsenal's failure to sign Ba.
It's similar to the Rooney deal in the sense that, with Torres, Ba and Romelu Lukaku, did the Blues actually need another striker? Probably not.
But even for £40 million, to take a player of his quality away from Manchester United would mark a significant signal of intent from the Blues, and psychologically, it could have given Chelsea the upper hand in the title race.
For the time being, Mourinho has been defeated in his ploy to prize Rooney away. A player of Eto'o's quality will suffice for this season, but Chelsea's interest in the Liverpudlian still very much remains, and this saga is far from over yet.