All Neo had to do was let Smith assimilate him. Then, the machines would do their thing to eliminate Smith.
So why did Neo fight Smith for so long?
Did Neo have real hope that he might kill Smith during the fight? Did Neo fight for long just to “trick” Smith into assimilating him? Is there any way to know?
Neo didn't realize what he had to do until after the fight. In the end he let Smith assimilate him because he finally realized it was inevitable. Neo even acknowledged Smith was always right
shareBut Neo goes to the machine center before he fights Smith. Why? Because he knew that the machines could delete Smith once he lets Smith assimilate him. Therefore, Neo knew what he had to do - He knew he had to let Smith assimilate him. Otherwise, Neo wouldn’t have gone to the machine center before fighting Smith
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Neo only realized that he has to let Smith assimilate him, when the Oracle speaks from Smith. If she can rule Smith such a way, then Neo could overrule him.
From that, it's choice like pazuzu said. And by than he understood his decision therefore he could look past by it and knew he could do it.
He maybe knew what he has to do when he went to the machines, because that was his purpose (to go to the source), but he couldn't see what exactly he has to do. Until he understood it.
(He learned this lesson when he dreamt about Trinity's death.)