In the story missions you stop the hive from wakening crota and bringing him to our material world. After you banish crota´s soul the only thing left to do is go deep into the hellmouth and finish him in his spiritual world, thats basically what you do in crota´s end.
But the only thing i dont understand is why crota killed thousands of guardians and then only six are necessary to kill him.
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Its because in his nether world he is mortal and can be killed when crota went against the thousands of praxic disciples he was an immortal shadow summoned by the hive through veeeery dark rituals and sacrifices
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It depends, but a strike team can be more effective than an army in certain situations. Six Gaurdians are able to spearhead into the Hellmouth and hit hard, while a large group would require a lot of coordination and would probably cause more problems than fix them.