England, on the other hand, will be happy with their batting exploits in the second ODI and Joe Root's return to form in the second ODI.
While Dhoni went past 10,000 ODI runs during the second match in Lord's, he was heavily criticised for his 59-ball 37.
England thrashed India by eight wickets with 33 balls to spare, a victory far more straightforward than anyone could have expected and one of the most rewarding since the last World Cup.
England then missed a chance to dismiss Kohli when the India captain, on 23, edged a drive against off-spinner Moeen Ali only for wicket-keeper Jos Buttler to drop a hard catch.
Left-arm medium-pacer David Willey (3/40) also claimed three wickets to contribute to his team.
He bowled India captain and star batsman Virat Kohli (71), as well as dismissing Suresh Raina, on his way to three for 49 in a maximum 10 overs.
Willey, who took three for 40 in nine overs, received excellent new-ball support from Durham quick Mark Wood (one for 30). India had a fine start, they won the 1st ODI but lost the 2nd.
Should Roy be unavailable it is expected that James Vince will come into the side with Billings there as squad cover for the match at Headingley.
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Morgan added: "I think we were outstanding". The soundest strategy may be to let him be until the 2019 World Cup is over since he has become such a crucial weapon for Morgan.
Meanwhile Kohli accepted his side had been outplayed. England were rarely troubled, bringing up 100 runs within the 15-over mark at Headingley, making the most of some sloppy fielding by India.
After Morgan won the toss, Rohit Sharma, who scored a superb century during India's eight-wicket win in the series-opener at Trent Bridge, struggled to make two off 18 balls, his innings ending when he flicked Willey to Wood at deep square leg.
WICKET! Adil Rashid has a "you miss I hit" moment as Dinesh Karthik is clean bowled for 21 runs.
Kohli pressed on, however, completing a 55-ball fifty before Rashid struck twice in six balls as India slumped to 158 for five.
Kohli backed up to a delivery that turned from leg stump and knocked over his off stump.
He was drafted in after Jason Roy was a doubt after suffering a finger injury during England's win at Lord's on Saturday.