Before the standing ovation, the latest milestone for his already impressive portfolio of achievement and more praise from his manager, there was a brief point when it had actually threatened to go horribly and almost absurdly wrong for Wayne Rooney. He had just wasted the most ridiculously straightforward opportunity to play in Robin van Persie for 2-0 and he could be seen holding his head in embarrassed anguish when Bayer Leverkusen conjured an equaliser out of nowhere.

But then the first Champions League tie of the David Moyes era took another twist. It finished as Rooney's night and, in the process, it felt completely incongruous to remember it was only a few weeks ago that large sections of the Old Trafford crowd were not even sure they would ever see him in United's colours again.

Van Persie restored Manchester United's lead and, in the 70th minute, Rooney hared away to score his second of the night. These were the 199th and 200th goals of his United career, establishing him as the fourth player in the club's history, after Sir Bobby Charlton (249), Denis Law (237) and Jack Rowley (211), to reach a double-century.

He had played with distinction, also setting up Antonio Valencia for United's fourth, and the most revealing moment was probably late on, with the game won, when he could be seen going up for a high ball, as if oblivious to the fact he was still wearing a protective band to cover up his stitched forehead. At times over the last few months it has felt like Rooney has wanted nothing more to do with this club. Nobody, however, could doubt his application on the pitch.

Moyes is plainly now getting the benefits from the club's intransigent refusal to do business with Chelsea. This was the proof that stance always made perfect sense. There was also a good strategy behind Moyes's decision to substitute the striker near the end. If the rapprochement is not fully complete, the crowd's acclaim will have told Rooney he is still hugely cherished. The one person not standing up was Sir Alex Ferguson, in the padded seats – though, to be fair, the previous manager is still recovering from hip surgery.

At times, this was the Rooney of old, hurtling past players, confident in his own running power, playing just behind Van Persie but with a licence to roam. His first goal should never have been allowed, with two offsides unnoticed and Valencia clearly impeding the Bayer Leverkusen goalkeeper, Bernd Leno, as Rooney volleyed in Patrice Evra's cross. The injustice, however, did not change the fact Moyes's team were deserved winners.

Moyes could also reflect on a reasonable performance from Marouane Fellaini before the new signing came off with cramp, on his first start, and though David de Gea will not enjoy the replays of Ömer Toprak's late goal to make it 4-2, after punching thin air at a corner, the more important moment was his save from the substitute Lars Bender just before punting the ball up the pitch for Rooney for goal No200.

They could easily have scored even more, too. Van Persie, of all people, missed a gaping chance and, most incredibly, there was that moment early in the second half when Toprak slipped and Rooney was clean through. Rooney's first mistake was to try to go round the goalkeeper rather than square the ball to Van Persie for a simple finish. But, having pretty much eluded Leno, the really shocking part came next. Van Persie was waiting for a tap-in and Rooney's pass – or maybe it was a shot – was horribly misdirected, straight out of play.

It was an astonishing piece of wastefulness and, within two minutes, Simon Rolfes equalised with a peach of a shot – beautifully measured, starting outside the post before curling inside the post and leaving De Gea rooted to the spot.

Sami Hyypia's team had knocked the ball around well but never truly looked like they believed they could win and the former Liverpool defender talked afterwards about the Bundesliga players perhaps paying too much respect to their opponents. They impressed in pockets of the match but they were always vulnerable in defence and United's response to the goal was particularly impressive.

Just before the hour, Valencia surged down the right and, though the cross was going slightly behind Van Persie, he improvised brilliantly, hooking a right-foot shot goalwards. Leno made a hash of his save and United were back in front.

Then it was Rooney's moment. Emir Spahic's poor defensive header, from De Gea's long kick, went straight to the forward, running through the inside-left channel. He picked his spot with an angled right-foot drive just inside the near-post.

Among his tributes after the match, Moyes talked about the way Rooney, on at least two occasions, trusted his own speed and determination to beat defenders. He also referred to the lovely weight of Rooney's pass before Valencia rifled in the outstanding goal of the night.

Valencia had one of his better games and Shinji Kagawa showed some nice touches on his return to the team. More than anything, though, this was a night that showed why the Premier League champions had been right to keep Rooney against the player's wishes. Happy or not, one thing has never changed: the latest member of Old Trafford's 200 Club is a formidable opponent.