If you are reffering to the Naruto from the Pain Arc, no, he definitely could have not beat him alone just with sage mode, he had all the possible advantages during their fight and still it was almost not enough:
1 - Konan noticed just before the fight that when Naraka resurrected the Pain bodies they were overcompensating and recovering way slower than before, which suggest some hinderance to some level, a moment before she also mentioned how Nagato have been wasting so much energy in fighting Konoha and in his last attack that he probably made his life shorter.
2 - Deva Path at first was drained and without function for a considerable long time for using his massive Shinra Tensei to destroy Konoha, so he couldn'taid his other bodies with his powers and in fact they had to check on him.
3 - Shima was the one who summoned everyone, Fukasaku, Gamabunta, Gamahiro, Gamaken, Gamakichi and Naruto himself, If at that point Naruto had to do all of that alone he would have wasted a lot of chakra which surely would have affected his performance during the fight, that even counting If he could have done that in the first place, even with sage mode, I dunno If he could have summoned more than Gamabunta and other of the Toad bosses being very generous, Fukasaku and Shima by themselves took an awful a lot of effort and time just for someone like Jiraiya (Naruto at this point had now a better control due sage mode and more chakra but still they were a lot of toads and Naruto was reserving energies for the Rasen Shurikens) and Minato could only summon Gamabunta at the time.
4 - Between the intel recolected by Jiraiya that Fukasaku taugh him and the one that later Katsukyu gave him, Naruto had a lot of information of the techniques and secrets of Pain while Nagato had none of Naruto.
5 - Naruto left two shadow-clones at the Mount Myoboku with sage mode because once they were summoned he would recover his energy and sage mode once lost, despite that this was his own idea Naruto only took to meassure because of the intel he had of Pain at that time knowing that he would need more than one sage mode to defeat him and Fukasaku was the one who summoned the first clone while Gamabunta distracted several of the Pain since restricted Deva was about to stab Naruto, so we know that If he had been alone Naruto maybe would have not take that preparation and even If he did it would have been very hard for him to summon his clone alone having all Pain attacking him simultaneously
6 - A lot of the successful kills and countermoves of Naruto during the fight involved direct actively partcipiation of the five toads, the three giant bosses and the two great sages toads, it was never remotely close of a 1v6 and again, Is hard to believe that Naruto could have summon more than one or two by himself without the chakra of Kurama which he could not control at that time without falling into the control of the fox.
7 - There are even those who claims that the first kill of Naruto against the Asura Path was thanks to Pain being distracted and facing with Tsunade and he was catch off guard, which has a little bit of truth and not means that Naruto would have not kill him later but it would have been one more problem to face off later if Pain and Naruto were facing in neutral ground.
8 - Despite all the advantages, Sage Naruto still was defeated and the toads stomped once Deva recovered his power and he got saved by Hinata, mind that in a neutral scenario like the thread suggest Naruto not just he would not have the help he had here but he would have faced this Pain from the start.
9 - Once Hinata got easily dispatched, Naruto is saved once more this time by the Kyubi who fought Pain and still Nagato managed to dominate the sixth tails and even had the eight tails struggling inside his moon, Kurama then almost took all control of Naruto so in each scenario he was fucked.
10 - Naruto is saved a third time by Minato nonetheless, and when Naruto came back he is fully healed and in Sage Mode when Deva stands extremely deteriorated and Nagato was few steps of death.
With all in consideration above (I had my doubts with point 7 but I bring it to take into consideration) how a Sage Naruto with no previous intel, only one summon, no the shadow clone prep on Myobuko and any exterior partcipation would stand against the Sixth Path of Pain fighting at the same time while being at 100%? He would get crushed, either Naruto resorts of Kurama and repeats all the previous seen game except that Minato would not be there and he would get consumed, or Naruto attempts to use the strategy of Jiraiya and fighting while he constantly retreats or plays hide and seek with them, but the scenario not plays in his favours and the elder toads would not be with him, not to mention that Pain would not fall for that again and he would unleash everything he has, he is also smart, so even Naruto would have to use all his strategy with the risk of being outsmarted by Pain, but seeing how it went still with all that help he would get stomped.
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