After the battle of Granicus Alexander split up his army: he left Parmenio behind with the main force, while Alexander himself went south with a smaller force. He travelled southwards along the coast of Asia Minor. From there he went northwards again, deeper into Asia Minor, until he reached Gordium where he joined the main force again. The only strategic reason for this small expedition might have been that he wanted to secure the coast of Asia Minor. But why did he not use his complete army for this? However, you must realise that Alexanders journey was often also an exploration, and sometimes even a pilgrimmage. He wanted to see and learn as much as possible from an empire which he considered his already.
With his complete army he marched southwards again, into the Cicilic plains. Now he formed a serious threat for Lybia, and also for the heart of the Persian empire and Darius knew that he had to come into action quickly. He was lucky as just at this time Alexander got the flu, and he had to stop his journey for a while.
Phase one: Darius taking the initiative.
Encouraged by the sudden pause in Alexanders journey Darius marched out with his immense army. He had chosen his route very well as he slipped past Alexanders army without anybody noticing him. Finally he moved through a northern mountain-pass and entered the plains of Issus. Alexander had left many men behind in this city who had become sick just like him. Darius showed no mercy and killed every single one of them. Now Darius had positioned himself between Alexander and the Hellespont: Alexander would get serious problems with his supplies, and there was no way back to Macedon...
Alexander was surprised by this sudden movements of the Persian army and he realised again that he had a worth opponent. Darius was not just a great organizer like most Persian high kings, he was also a great commander. Nevertheless Alexander never lost his nerve as Darius had made a big mistake in spite of his genius movement: he was in a small area which was caught between the ocean and mountains. In this small area Darius could never use his 600000 men optimally.
The position which was chosen by Darius looked a lot like the battlefield at Granicus. There was also a river at Issos, but it did not hold any water at the moment as it was the end of autumn. Still, even a dried up river formed a barrier which could slow down the enemy. The river Pinaros became thus a part of Darius' plans. He had been thinking about his tactics for a very long time, and it must be said that he used his troops in a very smart way. He placed his hired hoplits behind the river while light troops and cavalry formed a shield on the other side of the river.
Like said before: Darius had used his forces in a very smart way. Really, his only problem was that he was not fighting an ordinary person: he was fighting Alexander the Great. Alexander had a very mobile army like we know and he sent light troops from his right wing into the mountains to neutralize the Persian light forces there. He also sent a part of his heavy cavalry from his right wing to the left wing to stop the expected attack of the Persians cavalry. However, he made sure that he had enough cavalry left on the right wing for a concentrated charge.
Alexander has two options at this moment: he could attempt to encircle the Greek mercenaries with his cavalry or he could let the Greeks break through and encircle his army. He can not retreat with his cavalry to fill up the gap as then the left wing of the Persian phalanx could attack the Macedonian phalanx in the side. On the left wing the situation is also critical for Alexander. His cavalry seriously outnumbered and is having a really hard time to stop the attack of the Persian cavalry. The Macedonian formation almost falls apart when Alexander sends in light forces to help the cavalry. With the help of these slingers and javelin-throwers the left wing managed to maintain their position.
The Macedonians gain confidence when they notice that Alexander had forced a gap in the Persian formation, and the left wing of the phalanx managed to cross the river Pinaros. The Macedonian cavalry on the left is still in the same position as at the start of the battle, and the Persian cavalry is almost encircled by Macedonian light troops because of the sudden advancement of the phalanx. The word about Darius' flee spreads out over the battlefield, and the Persian left and right wing collapses. The center still holds its position until Alexander attacks it in the rear with his cavalry.
The results of his battle.
Darius managed to get away thanks to his fast chariot, but his mother, wife, and children are captured by Alexander. The most obvious strategy would have been that Alexander would move to the east together with his army and the royal hostages, to the heart of the Persian empire, before Darius had the time to recruit new soldiers. However, he was determined to fulfill his first plan: he had to gain control over the coastal areas. He made a very wise decission as the Persian and Cypriotic fleet were not only still in Persian service, but they were also still able to launch an attack against Macedon. Then Alexander would have to face the bizare situation of two countries whose armies were occupying the other country.
Alexander moved southwards down the Syrian coast and Sidon and Byblos surrendered to him without a fight. Completly different was the situation at Tyre: the citizens acknowledged his leadership, but they refused to let him into the city. Alexander was not impressed by the city, which seemed almost impossible to conquer, and he started the siege. After a long time he managed to take the city, which was furiously defended by its citizens, and he continued his journey southwards.