Basic timeline (with what I understand it to be anyways): Part 1 anyways
6000-2500 BCE: Ancestors of Somali, Afar, Sidama and Oromo migrate to Ethiopia, probably from the Sahara which is drying out from a grassland to a desert. One group break off from the main migration and settle instead in Darfur, founding the Fur and Masalit peoples, and the Beja settle instead on the Nile and found the Kush kingdom of Sudan.
2500 BCE - 400 CE: The ancestors of Somali and Afar settle in the hot lowlands, which would be called Berberica or the Berber country. They lived in small clan kingdoms in the inland, and traded and interacted with the rest of the world from their trade ports like Avalites and Malao, trading African Blackwood (Ebony), Ivory, Tortoise Shells and especially Frankincense. The trade ports were not the capitals and centers of these kingdoms, only the commercial centers, the political centers were far inland. None of these locations, either inland centers nor trade ports, have been excavated. There could be dusty small villages or they could have been great capital cities, we don't know. During this era, Shingani in Mogadishu was founded by Ximyar merchants, as were an unidentified early towns in Lower Shabelle and Lower Juba, near Baraawe and Kismaayo respectively. These Ximyar colonies would eventually spawn the Zenj civilization.
400-696 CE: The collapse of Idolatry in Europe and the Middle East causes a collapse in the Frankincense trade which leads to the demise of the great trade ports of Berberica, and a decline in power of the two great mercantile powers that controlled it, Aksum and Ximyar. This is a "Dark Age" of Somalia because it is dark to us, we literally know nothing about the history of Berberica is in this period.
696-1000 CE: Mogadishu is conquered by the Caliph in 696, beginning the Islamic era in Somalia. Aksum's continuing political crisis leads to a collapse of the Aksumite empire. Aksum is abandoned and Adulis becomes a pirate port, as pirates overrun the Eritrean coast and begin preying on commerce in the Red Sea. The Caliph has enough after these pirates attack Jedda in 714 and sends a fleet and crushes the pirates and destroys Adulis. During this time, Beja tribes had begun to invade Eritrea and conquer the region. The Caliph builds a fort at Badi (modern Massawa) and basically installs a viceroy, and leaves the Beja de-facto in charge of Eritrea. They also ended up in control of the Dahlak Islands (which had been overrun with pirates) and the Caliph decides to use Dahlak basically as an island Siberia, exiling people there.
Around this time the Somali ethnic group is created when the first few Berberica tribes become Muslim (even today remaining pre-Islamic societies like Rendille refer to becoming a Muslim as "becoming Somali"). Islam spread up the Shabelle to the Harar area (the origin place of the Somali ethnicity) where according to Harari legend, the first Islamic leader, Haboba ibn Harar, established the first Islamic center in nothern Somalia at Harar in the 8th century. Until the 11th century, all Samaale Somalis accepted a single king and lived together in the north, but when Maxamed Da'uud was killed a successor could not be agreed to, and the Samaale kingdom broke apart and the clans began migrating far and wide to establish their own kingdoms. Absame migrated west and established a kingdom on the Awash river, Hawiye migrated southwest to the upper Shabeele, Sade migrated southeast, Ajuuran migrated from their original home at Berbera far to the south to Mareeg and the middle Shabelle. Gardheere migrated far, far to the southwest all the way to the Jubba valley, Dir migrated west to Abyssinia and Kombe stayed behind in the homeland.
1000-1270 CE: During this period, the migrating Somali clans settled down and established kingdoms, conquered their neighbors and expanded their domains. The Ajuuraan expanded up the Shabelle conquering the Zenj of Qalaafo and established themselves as overlord of Muqdisho. The Absame conquered the Argobba kingdom of Shawa, the city of Zeila, the Awsa oasis and the Awash valley, thus establishing the two major kingdoms that would define the next 300 years, Ifat and Ajuran. The Amhara overthrew the Xamtanga Agaw Zagwe dynasty established a strong state which began to come into conflict with Ifat and other smaller Islamic states in the area, in fact the Amhara and Ifat first clashed before the Zagwe dynasty had been overthrown.
1270-1332 CE: Until 1332, there was a struggle over which power would be master of Abyssinia, Ifat and its Islamic allies or the Amhara kingdom, but the Amhara kingdom would decisively defeat all their allies and found an empire dominating the highlands under Amde Seyon. Amde Seyon inherited a kingdom only slightly bigger than the Zagwe had ruled, and by the time he died he had reconquered virtually the entire Aksumite Empire, from the Red Sea coast at Adulis all the way to the Rift Valley. Ifat formed a grand alliance to defend their kingdoms from his advance, where the combined armies of Ifat, Fetegar, Sharka, Dawaro, Arbabni and Bale were all defeated by Amde Seyon and were subjugated to his empire.
1332-1429 CE: Ifat eventually rebelled against Amhara rule, culminating in a massive invasion of Ifat in 1403, where the Sultan was killed and his family fled into exile in Yemen, returning a decade later to reclaim their homeland. This would be the beginning of the Abyssinia/Adal wars. The Amhara occupied Somali territory all the way to Berbera and the Jigjiga area, with fortresses occupying strategic areas. The exiled Walashma declared a new sultanate, Adal. They recaptured Zeila in 1423 and decisively defeated the Amhara armies in 1429, recapturing Jigjiga, Harar and Awsa.
1429-1529 CE: For a century Amhara and Somali armies would battle indecisively, both sides struggling over the Awash valley. This would continue decade after decade until the rise of Axmed Gurey, who united all the Somali clans of the north in a massive invasion of the Amhara kingdom.
1529-1540 CE: Axmed Gurey along with a small force of Turkish musketeers defeated the Amhara decisively and occupied most of Abyssinia, the Amhara being reduced to Gojjam, Begmeder, Dembiya and the Simien mountains. The Portuguese intervened in 1540, bombarding Zeila and destroying the city, and fighting alongside the Amhara, a Portuguese musketeer shot and killed Axmed Gurey and his army fell apart.