His traveling and reaching the Place where the Sun sets (the West)
(So he followed a way.) Ibn `Abbas said that he followed different routes to achieve what he wanted.
(So he followed a way.) Mujahid said that he followed different routes, east and west. According to one report narrated from Mujahid, he said:
(a way) means, "A route through the land.'' Qatadah said, "It means he followed the routes and landmarks of the earth.''
حَتَّى إِذَا بَلَغَ مَغْرِبَ الشَّمْسِ
(Until, when he reached the setting place of the sun,) means, he followed a route until he reached the furthest point that could be reached in the direction of the sun's setting, which is the west of the earth. As for the idea of his reaching the place in the sky where the sun sets, this is something impossible, and the tales told by storytellers that he traveled so far to the west that the sun set behind him are not true at all. Most of these stories come from the myths of the People of the Book and the fabrications and lies of their heretics.
وَجَدَهَا تَغْرُبُ فِى عَيْنٍ حَمِئَةٍ
(he found it setting in a spring of Hami'ah) meaning, he saw the sun as if it were setting in the ocean. This is something which everyone who goes to the coast can see: it looks as if the sun is setting into the sea but in fact it never leaves its path in which it is fixed. Hami'ah is, according to one of the two views, derived from the word Hama'ah, which means mud. This is like the Ayah:
(We (Allah) said (by inspiration): "O Dhul-Qarnayn! Either you punish them or treat them with kindness'') means, Allah gave him power over them and gave him the choice: if he wanted to, he could kill the men and take the women and children captive, or if he wanted to, he could set them free, with or without a ransom. His justice and faith became apparent in the ruling he pronounced:
أَمَّا مَن ظَلَمَ
(As for him who does wrong,) meaning who persists in his Kufr and in associating others in worship with his Lord,
(we shall punish him,) Qatadah said, i.e., by killing him.
(and then he will be brought back unto his Lord, Who will punish him with a terrible torment.) meaning a severe, far-reaching and painful punishment. This implies a confirmation of the Hereafter and the reward and punishment.
وَأَمَّا مَنْ آمَنَ
(But as for him who believes), meaning `who follows us in our call to worship Allah Alone with no partner or associate,'
فَلَهُ جَزَآءً الْحُسْنَى
(he shall have the best reward,) meaning in the Hereafter, with Allah.
وَسَنَقُولُ لَهُ مِنْ أَمْرِنَا يُسْراً
(and we (Dhul-Qarnayn) shall speak unto him mild words.) Mujahid said, `(words of) kindness.'
Maududi - Sayyid Abul Ala Maududi - Tafhim al-Qur'an
"The limit where the sun set" does not mean the "place" of the setting of the sun. According to Ibn Kathir, it means that he marched to the West conquering one country after the other till he reached the last boundary of the land, beyond which there was ocean.
"He found the sun setting in black muddy waters of the sea": if Zul Qarnain was Cyrus, then that place would be the western limit of Asia Minor and the "black waters" would be the Aegean Sea. This interpretation is supported by the use of the word "`ain"instead of "bahr" in the Qur'an.
"We said to him" does not necessarily mean that Allah directly revealed to him these words, and that Zul-Qarnain was a Prophet or was the one who received inspiration from Allah, and the same is the reasonable conjecture. This concerns the time when Zul-Qarnain had taken possession of the land as a conqueror and the conquered people were utterly at your mercy. Then Allah posed a question before his conscience, as if to say, "Now is the time of your trial. These people are utterly at your mercy, and you have the option either to behave unjustly towards them or to treat them generously."