I figured it out....I know how the apes got the ship ready for flight
It's so simple. Time passed and Taylor was captured and healed. This took many weeks or months. During this time, I figure there must have been a dry spell in the Forbidden Zone. The lake dried up and revealed Taylor's ship which only landed in water. It was not destroyed and it did not crash. Dr. Milo must have made an expedition out there and reclaimed this oddity from the dry lake bed. He then began to study it and clean it of any unwanted dirt, water, and contaminants, but not informing anyone of his find for fear of being labeled a heretic since he knew this was something beyond what was known about in ape society and history. So he kept quiet and began to study it in some way. As he did this, he must have heard of the human running around Ape City and talking. He then investigated further about what was going on and heard about everything that Taylor had conveyed to Zira and Cornelius since he was the inquisitive type with a scientific mind. He deduced that the thing he had found was Taylor's space ship and made it his mission to understand it and how to operate it. Taylor gets sentenced in court and his escape is arranged. All the while Dr. Milo works on the restoration of the ship which was built to withstand the rigors of space and could easily withstand some water. Dr. Zaius and his henchmen have their confrontation with Taylor, Zira, and Cornelius in the Forbidden Zone and then Taylor rides off at the conclusion of that situation. Dr. Zaius and crew return from the Forbidden Zone and then Dr. Milo secretly informs Zira and Cornelius of his find and they decide to launch this ship as soon as possible. A week or so goes by as everyone prepares for the upcoming test launch. Brent arrives, but his ship is damaged beyond repair. Dr. Milo, Zira, and Cornelius plan and get ready for their test launch. As luck would have it, they launch and the Earth explodes, which hurls them back in time to 1973.
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