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.
“I have teachers from every single Arab country in the Arab world. Every single one...I have a teacher from one of the Arab countries. And my teachers were amazing”  – Shaykh Hamza
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):
1. Murabit al Hajj (Mauritania) 
2. Shaykh Khatri (Mauritania) 
3. Shaykh Abdullah bin Bayyah - Fiqh 
4. Shaykh Mohammad al-Yaqoubi (California) - Maliki Fiqh [XXV]
5. Shaykh Abdullah Ould Siddiq (United Arab Emirates)- Maliki Fiqh 
6. Shaykh Baya bin Salik (United Arab Emirates) 
7. Shaykh Bashir Shaqfah (United Arab Emirates) 
8. Muhammad Shaybani (Abu Dhabi) 
9. Hamad al-Wali (United Arab Emirates) 
11. Muhammad al-Fatrati - Al Azhar University in Cairo, Egypt 
12. Shaykh Ahmad Badawi (Sudan) - Hadith 
13. Sidi Bou Said (Tizi, Algeria) - Quran 
14. Shaykh Ahmad Dughan (Saudia Arabia)
15. Shaykh Hasan al-Ghimari
16. Shaykh Sayyid Ibrahim al-Hasawi
17. Shaykh Ahmad Jabir Jibran
18. Shaykh Abdullah al-Kadi (Saudia Arabia)
19. Shaykh Muhammad al-Kittani
20. Shaykh Muhammad Alawi al-Maliki
21. Sidi Bou Said (Bilal ibn Rabah Madrassa - Tizi Algeria) (Most likely Quran)
Of the Islamic Sciences he has studied: 
1. Arabic grammar, Morphology and literature
3. Hadith terminology and transmission
4. Qur'anic recitation (tajweed)
5. Theology (aqidah)
6. Fiqh: Maliki jurisprudence
a. Some of the Texts: al-Risalah , sections of Aqrab al-Masalik, al-Fiqh al-Maliki fi Thawbihi al-Jadid (Islamic Institute of al-Ain) 
7. Usul: Legal foundations
9. Dialectics: Adab Al-Bahth wal-Munadharah
10. Tawqit: Astronomy
12. Spirituality: Tasawwuf
13. Ibn Ashir
(I said to one of my teachers) "I really need to sit
And he said, "You have everything you need. Just go out and defend the Muslims, and Inshallah, Allah give you Tawfeeq." 
-Shaykh Hamza Yusuf (Seeking help after 9/11)
"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
"I think that the attack on Afghanistan is a tragedy, and that it is has very frightening consequences."  -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."