Between 1536 and 1540, Juan Rodriguez Cabrillo built seven or eight ships for Alvarado. Alvarado after returning from a trip to Spain, wrote to the King in 1539 saying that he had prepared an "armada to go on a voyage of discovery". He had planned to split his fleet of ships into two groups to explore both the Pacific, and the Northern coast of Baja or lower California.

Joining this fleet was the San Salvador, it was poised to be the flag ship of the coastal expedition. However, a sudden Native revolt had forced Alvarado to run to the aid of the colonists. During the fight, he was crushed by a falling horse. He lived a few more days before dying, possibly in considerable pain.

Alvarado had tried to pay Cabrillo for his work by giving him land, but ownership of that land was now being challenged by others. Cabrillo himself, had partially paid for the construction of the fleet on Alvarado's word that he would cover him, but now he was dead. Knowing he would have to appeal directly to the Spanish Crown for his payment, Cabrillo collected some statements to cover his butt and set sail for Guatemala for further instructions.

The Viceroy still wanted the trip to continue however, so by September 1541, Cabrillo made his way to a port town called Navidad, Mexico and finished preparing for his voyage. In June 27, 1542, a small fleet of two or three ships set sail from Navidad. The fleet was to sail up the Pacific Coast to continue Ulloa's expedition up the west coast of the enormous "island" that lay beyond the Sea or Cortes. The main flagship was the 200 ton galleon, San Salvador. The other ship was a 100 ton galleon named the "Victoria".

If you’ve seen a galleon, it makes you wonder how it or the people inside were able to survive at sea. They’re small, wooden vessels with multiple decks and masts. More sail than anything, and they don’t look very easy to control. It wouldn’t be fair to compare them to any of the ships that are active today (Well, except for the full size replica sitting in San Diego bay). I guess you can think of it as a slightly larger fishing boat made of wood and sails. As William E. Smythe put it:

The first five days of Cabrillo’s Expedition were uneventful, but on the 2nd of July, they had Baja California in view. Because of the bad weather though, it took them four days to cross over, anchoring at Punta de San Lucas. By the eleventh day, July 8th, they landed in an area called Punta Trinidad and waited for a storm to pass. They left Punta Trinidad on the 12th; passed Puerto San Pedro, and landed at a newly discovered port they called Madalena by the 19th. On July 20th they left Puerto Madalena. Stopping for food, water or firewood, they anchored at Punta Santa Catalina, Puerto Santiago, Punta Santa Ana, and Puerto Fondo. 

Beginning in August, they left for the next port, San Pedro Vincula. Then they would anchor at the Islas San Estevan, Islas Zedros, and Puerto Santa Clara. They noted that since reaching the California coast, they had seen no natives on the shore. The first time they saw any was a small group of four on the shore of Puerto Santa Clara, who quickly fled. Because of bad winds, they stayed there until August 13th. Two days later, they anchored at Punta del Mal Abrigo. By the 20th, they had left San Bernardo and landed at Punta Engano. On the 22nd, Cabrillo went to shore and claimed the territory for Spain, renaming the place Puerto La Posesion. They stayed for repairs until the 27th. On the 31st, they found group of native fisherman, three of which they hosted on the ship, but couldn’t understand anything they said by “signs” or improvised sign language, so they let them go. They did have luck with another group of indians though, who signed to them, saying there were other Spaniards about five days inland, possibly the remains of the failed Coronado Expedition. Cabrillo let the natives go with a letter to carry to the Spaniards if they ran into them.

In the month of September, they continued up the coast, anchoring on Islas San Agustin, Cabo de San Martin, and Cabo de Cruz before landing in Puerto San Mateo on the 17th. They left San Mateo on the 23rd of September and traveled along the coast some 18 leagues. They then passed by three uninhabited islands. He named them “Islas Desiertas”, Spanish for "desert islands". Beyond those islands, however, they saw clouds of black smoke coming from the mainland. People were living here.

September 28, 1542, fifty years after Columbus made his historic voyage, they traveled about 6 more leagues before finding what they recorded as “a port, closed and very good”. They wrote down the coordinates as 34^1/3 degrees and decided to set anchor at the mouth of the port, that was naturally covered in cobblestones between a raised hill, or as the Spanish call it "loma", and a couple of low lying sandbars.

In the Spaniard's attempt to please their god, much of the Spaniard’s discoveries were named after saints and biblical references. Saints have their own day of celebration, where great feasts are held. For instance, the feast of Saint Michael fell on the following day, September 29th. The Spanish referred to Saint Michael as “San Miguel”. So when Cabrillo and his fleet set anchor in this stable, natural harbor which they had never seen before, it seemed only appropriate for him to name the port “San Miguel”.

This is where our traditional stories of this territory usually begin, except despite Cabrillo's intentions, this land would later be known as "San Diego".

The Spaniards grabbed some articles to barter with and gifts to give, roped their sails, and prepared to go to shore. Because the bay seemed too shallow for the ships to travel through, a small group led by Cabrillo lowered a small boat and rowed toward the marshy shore. They soon began to see people on the shore. They noticed that the people had gathered to watch them, but those people soon began to run away as the Spanish rowed closer to shore, leaving only three natives on the suddenly lonely and quiet beach to greet them. They continued to row towards the shore anyways, and upon landing, claimed the land for Spain with their usual flags and chanting. Then, they stood to greet the three remaining natives, who seemed very frightened.

Cabrillo and his men wore colorful uniforms, armored with polished metal breastplates, helmets, swords and crossbows. They are backed by a country that just conquered an entire country. The three natives wore animal skins and painted faces. The rest of the natives, many of them simply butt-naked and frightened by the Spanish, had fled the area and were watching from a distance. Even if they did stand up to fight, their bows and arrows were no match for the Spanish powder and lead. They probably anticipated a slaughter of their people.

Instead of a slaughter though, Cabrillo and his men gave the three native people presents. The journal doesn’t say what they gave them; I’m assuming shirts. This may have surprised them all since they may have heard terrible stories from other villages of Guacamels, or white Christians, coming to kill and raid them to the south. Since neither group spoke the other's language, the natives used their best sign language to relate to Cabrillo that men looking like he and his men had passed through south-east of the mountains. The Ipai and Tipai wanted Cabrillo to know that they were afraid.

Overall, first contact was peaceful, so Cabrillo sent a few of his men up the river valley in search of fresh water, and a few others to gather fish. Day gave way to night, and the group sent to gather fish returned to the San Salvador with three of their men wounded by arrows... the first recorded instance of hostility. By the next morning, the men who were sent to find fresh water still hadn't returned and their shipmates were getting worried.

They hadn't been attacked however, they were simply lost. By the time the group had found water, it was night time. They retraced their steps back to the port by following the "drying out river" valley back, but literally took a wrong turn. When they reached what they thought was the same bay they had come from and didn't see the ships in the dark of night, they set up camp and spent the night there. There is no telling what must have gone through their heads at the time. They might have thought that the small fleet had left them stranded on the port. In reality, the men had reached another bay, north of the newly named San Miguel bay. It was easy to get the two bays confused; hence it would someday be given the name “False Bay”. Today, it is Mission Bay.

The journal summary is vague on the details of these events. The next morning, the men were found by another party that was sent out to search for them and were guided back to the ships. Another group took a small boat and explored the large, but shallow San Miguel bay. They decided to bring two native boys with them as guides, but they couldn't communicate with the boys through sign language, so they sent them away with some shirts.

A day later, three natives came to the ships and communicated with the Spaniards by signs. They reiterated that men dressed like them had traveled further inland, riding on horses, or “caballos”, but added that the men had killed many natives in those regions. They were afraid these Spaniards would do the same to them. The summary of the voyage doesn't mention what the Spanish said to the three natives, but he probably gave the natives a letter to send out to the party of Spaniards. It also tells of a heavy storm that passed over the area during Cabrillo’s stay. However, the bay protected the ships so well, it passed without incident.

Cabrillo and his men stayed in San Miguel for about 6 days before setting sail to explore the land to the north. The trip from that point wasn’t as smooth as expected however. Five months later, the San Salvador returned to San Miguel once again. Since they had last left, Cabrillo had passed away and the San Salvador had become separated from the Victoria. They spent six days at the port, waiting for the other ship which never arrived and left. The Ipai and Tipai would not see a ship again for another sixty years. In that time, parents would pass down the story of when the Guacamels visited Cosoy and the various other villages to their children and those children would grow to pass down that story to their own children. Life of the Ipai and Tipai would have gone back to normal, if not for the disease that most likely spread across the region after first contact.

Relation of the Voyage of Juan Rodriguez Cabrillo, 1542-1543
http://www.americanjourneys.org/pdf/AJ-001.pdf

William E Smythe's Chapter relating to the voyage
http://www.sandiegohistory.org/books/smythe/1-1.htm

Richard F. Pourade's chapters on Cabrillo and his voyage
http://www.sandiegohistory.org/books/pourade/explorers/explorerschapter3.htm
and
http://www.sandiegohistory.org/books/pourade/explorers/explorerschapter4.htm