Sam left Frodo because he thought that he was dead.
Shelob didn't kill him because she doesn't like to eat dead prey, they must still be alive - but Sam didn't know this.
After Sam went on to continue the quest (thinking Frodo dead) he heard Orcs assembling around where he had left Frodo. Now, the Orcs knew that he was not dead, so they kidnapped (in a manner of speaking) him and took him to their tower. There, they took away Frodo's clothes and left him locked in the topmost part of the tower. That's where Sam found him.
I imagine that when they found Frodo they stripped him because they were looking for the ring (but Sam had it, he he).
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