After 10 years overseas, Shaykh Hamza wrapped up his affairs and flew back to the United States. The barakah in his time overseas is apparent, as it seems he lived through several lifetimes. In all, he would have travelled through 7+ Countries, and studied under multiple teachers in each.
There are no details on why he came back to the US, but presumably he wanted to settle down, had completed his studies, or was told to do so by his teachers.
Whatever the reason, he moved to Imperial, California, a little outside of San Diego, right up against the Mexican Border.
He studied Nursing and English from 1987 to 1990, gaining an Associate’s Degree in Nursing and an Associate’s Degree in English from Imperial Valley College. During this time, he was also working on a post-graduate degree as a student of homeopathy, with the Devon School of Homeopathy. The Devon school of Homeopathy is in England, so presumably the work was completed via correspondence.
After finishing his degree, Shaykh Hamza worked in the Cardiac Care Unit of a Hospital. 
Presumably, much of Shaykh Hamza's experience in medicine, and his familiarity to Doctors and heart medicine was from this time period.[XXIII]
After some time working, he re-enrolled in University and completed his Religious Studies / Comparative Religions Bachelor’s degree at San Jose State University in 1997. Soon afterwards he would enroll again for a Master's Degree at Stanford, which did not start, was rejected, or was aborted partway.[XXIV]
In 1991, he received an Honorary Doctorate at Zaytuna University in Tunisia (conferred by Shaykh Shadhili Naifer).
From 1990 to 1995, Shaykh Hamza started to transition from full-time worker to part-time lecturer and then finally full-time Imam. For an unknown duration of time, Shaykh Hamza became the Imam at the Muslim community association of the Bay area and Santa Clara, California.
Shaykh Hamza also got married around this time. (He would have 5 boys in total as of 2011).
Very quickly, the Muslim community was able to recognize what they had in Shaykh Hamza, and as early as 1993, he was speaking at the National ISNA conference. He reflected on these times during ISNA's anniversary conference,
"When I look back and reflect on ISNA, I also have to look back and reflect on my own experience. Because, I've seen ISNA grow, but I've also grown with ISNA. I know the first time that I came here, to the ISNA conference, many years ago in 1993, which was a time when I look back on it, I was far more assured about myself then I am today. I think that I have a lot more certainty about Islam, that has grown, but the certainty I had about my own understanding, I think, has diminished.
Islam has become a much vaster thing to me. It has become bigger, then I understood Islam. When I first began speaking at ISNA…I know I can speak with certainty about Dr. Syed Syed. He must have thought I was crazy. But he was also very welcoming to me. And I want to take one moment of remembrance of our dear brother Dr. Mahboub Khan, Raheemullah, who really was the reason I started speaking at ISNA,
…He was somebody who, and He said to me once, I don't agree with a lot of what you say. But I know you're good for Islam in this country.
So even though he had his own reservations, about some of my attitudes, which I think were probably justified at that time. But despite that, he was also very encouraging."
Aside from ISNA speeches, he was also personally involved in Deen Intensives and Rihla's. Teaching students lucky enough (or smart enough) to know of him and able to attend his camps / programs.
After extensive work in the community, as Imam of Santa Clara Mosque, and giving talks and lectures around the country, Shaykh Hamza put his plan in place, and in 1996, he joined with Dr. Hesham Alalusi to found "The Zaytuna Institute".
It would not be until 1998 that they broke ground in Hayward, California and established a physical building. The building was purchased for $750,000 and needed a lot of work for use.
In its own words: "Zaytuna Institute is a non-profit, educational institute and school founded and run by people committed to reviving time-tested methods of educating and transforming human beings. It is our belief that Islam offers a cohesive understanding of the world and a praxis for it that is able to cut through the illusion of contemporary nihilism and materialism."
About 2008, when the new Zaytuna College building was completed close to Stanford, the original Zaytuna building was closed down.
It's difficult to identify all of Shaykh Hamza's teachers, as he travelled so much, and mentioned so few of his adventures. Of his known teachers (In no particular order):
Of the Islamic Sciences he has studied: 
"Afghanistan is probably one of the greatest crimes against humanity…certainly in modern history. It's not less tragic then much of what happened in World War II"
- Shaykh Hamza Yusuf
And then two airplanes were crashed into the World Trade Center.
Many events occurred both before and after 9/11; the simplest explanation is that Shaykh Hamza did what he could during that chaotic time period. The US was in shock and marching towards war. It was a difficult time for all Muslims in the West.
He has been attacked roundly by Non-Muslims and Muslims alike for his actions and statements during that time. (Some of his own acquaintances would admonish him publically for some of his statements.)[XXVII]
Speaking of that time, Shaykh Hamza reflected later about life before and after 9/11,
"On Sept 11, my life was changed very radically; I thought I had a busy life before Sept 11. It was actually slow, calm and enabled me time to reflect and time to think about things at a deeper level; What I found after September 11, things began to move so quickly that I really missed the opportunity of just being able to sit back and deliberate."
"I would say in terms of the response of the United States, I was deeply troubled by it, I think it was a very aggressive and really in many ways, I don't think it was justifiable" -Shaykh Hamza Yusuf
Seven days after the Twin Towers fell, President Bush requested to meet with a Muslim leader. A Muslim aide in the White House knew Shaykh Hamza personally, and he contacted Shaykh Hamza requesting him to meet with President Bush. [XXVIII]
Shaykh Hamza thought about the request, and after speaking with Shaykh Abdullah bin Bayyah on the matter, he went to the White House.
In parallel, while Shaykh Hamza was in Washington, the FBI sent several agents to his house to question him regarding some statements he had made earlier that year.
"He isn't home," said his wife. "He's with the president."
The FBI agents did not seem to believe her; they called the White House to check.
"He's got 100% security clearance," said the voice at the other end. The FBI agents did not return.
Back from Washington, Shaykh Hamza organized a talk to explain what had happened at the White House. The lecture was given away free by Alhambra Productions at that time.
"It was a very difficult trip. I was asked by somebody I know. People probably know he's working in the White house. He's a Muslim, son of a very prominent Muslim.
He called me up and said, 'They're asking for somebody to come and talk to the President, and represent the Muslims'. And he said, he thought that I would be the best person, in my estimation, "So can you do that, can you come?"
I talked to Shaykh Abdullah bin Bayyah. And he said it was a Fard on me, "You have to go."
I went, and I was part of about 30 religious leaders there. The Head of the Mormons was there, Head of the Franklin Ministries, his son Franklin Graham. The Archbishop of the Greek Orthodox Church, the Archbishop of the Catholic Church in America. Just a lot of prominent religious leaders (were there): The Tibetan lama, there was one of the Heads of one of the National Sikh Organizations and a Methodist Bishop, a lot of different people.
From that group, a handful, six of us, were asked to meet with President Bush in the Oval Office.
I put forward 4 points. We were given quite a bit of time, I was allowed to say all the points that I wanted to say.
I gave a copy of the "Essential Qur'an" and I had spent the night before going through it and putting stick'ems on all the verses that I thought were the most pertinent. I said, 'I know you're very busy, so if you don't have time to read the whole thing, read these verses.'
And then I gave him a book, "Thunder in the Sky", which is a book that Thomas Cleary translated on the humanistic use of power. How to use power to benefit humans and not to harm them. I also gave him a piece of Calligraphy that Mohammed Zakariya did (he did the Eid stamp).
When I called him (Mohammed Zakariya), he's in Virginia, he lives a few miles away from the Pentagon, he was writing what's called a Hilya in calligraphy, from the Shifa of Qada Yad, and it was a description of the Prophet SAW from Amr bin Al-Aws. When he heard the explosion, he told me the sentence he was literally writing was, "He would never repel an evil with another evil. But he forgave and he condoned."
The beauty of this, is that only Allah can do this. That's for Mohamed Zakariya, because Allah is the Author of this. Allah is the one who has decreed all of this. And that was for Mohammed Zakariya. It was a moment for him, and then it was related to the present.
That's our teaching, that's his description, and that's why we know that no matter what America has done to Muslims anywhere, our teaching is that we don't pay evil for evil. And that's Islam, it's not all this rage and anger that's out there. That is Islam, and it's a hard thing to do, but when you remember, that this is dunya, and you're looking at infinity, you're not looking at dunya, you're not looking at 50, 60, 70 years, you're looking at infinity. And you want Allah to forgive you for your own evil.
Isn't that what we all want? We just want forgiveness on Yuom al-Qiyyama (The Day of Judgment), because we're all guilty.
We think that we're independent of Allah. We're all guilty from that perspective. But the point is, here he is writing that, and I told him (President Bush) that, "this is what he was writing, when the Pentagon was struck, 'That he does not repel an evil with an evil.'"
That's the beauty of our Deen. That's a true story, it's not made up. Because, Mohammed Zakariya is a true Sadiq, He's Truthful, he doesn't lie. And I believe him, I don't need any witnesses, the angels were the witnesses. Those are our two just witnesses.
The points that I made, the first was emphasizing and that it had to be reiterated again and again that Islam does not have anything to do with this. That this is not the teaching of Islam, it's the religion that teaches mercy, compassion and when it uses martial force, it uses it with just laws. Non-combatants are never involved.
It's based on legitimate authority, not on vigilantism. We don't believe in vigilantism, we don't believe in outlaws.
We don't believe in Robin Hood. It's kind of interesting: in this culture, Robin Hood is a hero. He stole from the rich and gave to the poor.
Then even more bizarre, and I told them this on 60 minutes, I doubt they'll put that on there. I said Samson is the first suicide bomber, and he's in the Bible. If you don't know the story of "Shamsoon", Samson was in the temple of the Philistines, he was an Israeli. He asked, 'where are the pillars that hold the temple up?', and he goes and in chains, he pushes them, killed himself and everybody else. As revenge for the Israeli's against the wrongs of their enemies.
I was taught that as a child, he was a hero. That's not in the Qur'an, it's conspicuously absent from the Qur'an.
The second point was the danger of Polarization. That this could polarize the world. And we could get a self-fulfilling prophecy of Samuel Huntington's 'Clash of Civilizations': China, Islam vs. the West. Nobody wants that, there is no benefit in that, except for warmongers. People that make money off of the death of other people.
And then the idea of consensus. I had already talked to Shaykh Abdullah bin Bayyah, and I also conveyed that to some Arab Ambassadors, that I felt that there should be a summit meeting of the most prominent Muslim Ulema in the Muslim world to declare Terrorism as inconsistent with the teachings of Islam and that it is prohibited by Ijma and that there should be an Ijma of that.
This should be rejected, and I also suggested that there should be one done of the Abrahamic religions in somewhere like Rome or Jerusalem or somewhere there's a declaration that it is not consistent with the teachings of the Prophets the taking of Innocent lives, whether it is State Terrorism or individual terrorism, it is rejected by religion, and let them be seen as what they are: political means to political ends.
That's not what the Prophet's came to teach. They came to teach Prophetic means to Prophetic ends.
The last was about oppression. That this country had a responsibility in creating just regimes because of the power this country has. That we have to recognize the oppression and extreme circumstances in the Muslim world that breeds the type of extremism that exists in some parts of the Muslim world.
I think that Muslims are incredibly moderate. I think the Iraqi's have displayed incredible patience and perseverance and lack of animosity and hatred. I think the Muslims are a testimony. One thing, Ismail Faruqi said, he was in debate once, and I heard this from somebody that was present and a man he was debating was just saying how terrible the Muslims were and Ismail Faruqi said, "You see the Muslims now with their corruption, and you go to their countries and you can laugh at how corrupt these countries are and despicable, but have you seen us suffer? Have you seen what happens to us when we get afflicted with pain and suffering? Then you'll know who we are".
He said "because when we lose all our money we don't jump out of buildings". We say "Mashallah, La Kuwata illa Billah". And that's the truth. You know the Muslims have been incredibly patient in the light of all this….
…I was asked to be the guest that night, of the First Lady, and I was told that there was going to be a speech, I had no idea that it would be, the way it was, I really didn't. But that's the situation I was in. And my intentions in it were trying to do what I could do, in this type of crisis. I mean you just, you have to do what you think is the right thing and the best thing for the overall benefit and I would say not just for Muslims but for everybody. Al-Mas lahul-ama. Because we have a concern for humanity in general, and certainly for the Muslims in particular.
Always, the Ummah is paramount, but we're also supposed to be caretakers of humanity. That's a task that we're given by Allah. So we should not act without the rest of humanity in our considerations.
Something that I really want to emphasize here, I thought that the most profound person and the one that seemed to be the most genuine person of all these people that I met, was Rabbi Joshua Habberman. What he said to Bush, he defended Islam.
I looked over at him, we were In this room, it was the Roosevelt room or something, and there was all these (dignitaries there)…Mayor Giuliani was there, and the Governor of New York, and the chief of staff and all these big (people), and he was sitting in a corner reading something in Hebrew. Everybody else was smoozing and doing all that.
I went over and sat next to him and said "What are you reading?"
He said, "I was reading the Psalms."
He was, he just seemed like a genuine person. We spoke quite a bit, He felt most comfortable (with me) I think.
He just said "You know the tragedy of this, is that American's are so ignorant of Islam. And they don't know the greatness of the Civilization, they don't know history and they really think this represents in anyway, Islam."
He said, "This is the real tr