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Signed on a season long loan from Birmingham in August 2012, as part of the deal that saw Paul Caddis move to St. Andrews, Rooney stated that he had been lured to the County Ground by the Town’s impressive results in the opening weeks of the campaign. After sitting out a bizarre 4-1 defeat at Preston on the bench, Rooney made his debut in 1-0 defeat at Oxford in the Johnstone’s Paint Trophy, playing in an unusual position on the left flank. The following weekend, Rooney made his league debut for Swindon, coming on as a second half substitute in a 1-0 home defeat to Leyton Orient - the following Saturday, he netted his first goal in a Town shirt on his first League start - a twenty yard strike in a 2-2 draw at Carlisle.
Rooney struggled to make an impression on the Town’s starting eleven - boss Paolo di Canio clearly preferring James Collins, Andy Williams and Paul Benson in the opening months of the season, restricting Rooney to substitute appearances - and though he netted further goals in 4-0 wins over Bournemouth and Stevenage, di Canio accused the striker of having arrived at the club with no fitness level - Rooney himself admitted that he wasn’t pleased with his own finishing, having squandered chances against Coventry and Scunthorpe in October that would have sealed victories for the Town. When he did start two games in October and November, both ended in defeat - at Crewe in the League, before being withdrawn at half-time in an embarrassing defeat against Macclesfield in the FA Cup. Di Canio described Rooney’s performance in the cup defeat as “poor”, and utilised Rooney just once over the next three months - after signing striker Chris Martin, the Town started to push for promotion, and Rooney found himself on the sidelines.
At the turn of the year, there was some doubt as to whether Rooney would remain at the club, after Paul Caddis agreed a permanent switch to Birmingham - but di Canio was adamant that the striker would remain at the County Ground - still though, it took the Town being in the middle of an injury crisis after the shock sale of Matt Ritchie before Rooney featured again - and after coming on as a substitute in a televised clash at Crawley, Rooney won a soft penalty, stepping up and slotting it home himself to earn a point for the Town.
With Martin now departed, and the Town in the midst of a takeover and transfer embargo, di Canio had little choice but to utilise the striker - and Rooney started back-to-back games against Colchester and Hartlepool - Swindon failing to name a full sixteen for any of the matches in which he had returned for. Days later, di Canio resigned, citing the sale of Ritchie and broken promises from both the departed and incoming board members - caretaker managers Darren Ward and Tommy Miller naming Rooney on the bench for the two games in which they took charge - the Irishman netting an equalising goal in a 1-1 draw with Preston just a minute after entering the fray.
When the new board was finally in place and new boss Kevin MacDonald appointed, he left Rooney on the bench for his first two games, before naming him on the right side of a 4-5-1 formation at fellow promotion chasers Brentford in mid-March. A week later, he swapped Rooney with lone striker Andy Williams in the same formation at Yeovil in another promotion clash - Rooney netting a second half penalty in a 2-0 win - but when the Town failed to break down Notts County the following Saturday, Rooney was benched again the following weekend - but he came off the bench to net an equaliser in a 1-1 draw with Oldham. Slowly, Swindon were dropping out of the race for automatic promotion - and after three defeats in a row at the beginning of April, Rooney returned to the attack again for the visit of Crewe - and he netted twice in a 4-1 win that all but sealed the Town’s place in the play-offs.
Rooney’s fortunes were mixed in the end of season finale - after missing two one-on-one chances in the opening leg against Brentford, he was attributed with an own goal in the second leg to put the Bees ahead in the tie - before netting at the right end to get the Town back into the game. After being withdrawn early in the second half, Swindon dramatically came back from 3-1 down to draw the game 3-3 deep into injury time, before losing the penalty shoot out.
After the season ended, it was revealed that Rooney’s loan deal included a clause that would invoke a two year permanent contract starting the following season - costing the Town a staggering £8000 per week including bonuses, agent’s fees, living expenses and other add-ons - a hangover from the free-spending previous regime. Though chairman Jed McCrory stated that he wanted Rooney to remain at the club, he admitted that the board questioned the validity of the contract and were trying to renegotiate the deal - and as the saga went on over the summer, the striker was turned away from the training ground after reporting for pre-season. The following week, it was confirmed that the striker was training with Oldham while the contract dispute was ongoing - soon after, McCrory stated that they were waiting for feedback from Rooney, who also took advice from the PFA. McCrory later revealed that the initial contract had remained unsigned by certain parties in the deal, which the club felt made the contract void - and at the beginning of August, Oldham confirmed that they had signed the striker on a two-year deal. It was the following March before the contract dispute was finally settled - with an FA tribunal originally set to hear the case in January, before postponing it until June, the two parties came to a resolution in advance of the new date - the club believed to have paid the striker a six figure fee in the region of £140,000.
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