From 1941 to 1945 a bunker beneath Magee College was part of Base One Europe, the Allied command network coordinating the Battle of the Atlantic. The Derry bunker linked to Derby House in Liverpool and Whitehall in London, and together these three rooms controlled the movements of around a million Allied personnel hunting Nazi U-boats. Derry's location at the northwestern edge of the United Kingdom made it the closest deepwater port to the convoy routes. Wrens - members of the Women's Royal Naval Service - operated much of the equipment. Dame Alice Rosemary Murray, later the first female Vice-Chancellor of Cambridge University, was stationed as WRNS Chief Officer responsible for the welfare of 5,600 Wrens in Londonderry. There is a strange family thread running through Magee: Lady Winifred Peck, mother of Julian Peck of Prehen House just up the river, was the sister of Dilly Knox, who directed Bletchley Park's code-breaking. The intelligence war and the academic war passed through the same small set of families.

In 1953 Magee broke its formal links with Trinity College Dublin and became Magee University College, with the obvious ambition of becoming Northern Ireland's second university after Queen's in Belfast. Local groups led by the University for Derry Committee campaigned hard. Derry had the buildings, the tradition, and the need - a city of 60,000 with no university of its own. In 1965 the Lockwood Report, written by Sir John Lockwood, Master of Birkbeck College London, recommended placing the new university in Coleraine instead. The decision was passed by the Stormont Parliament and remains, in Derry, one of the great wounds of mid-century unionist governance. Many in the city believed - and still believe - that Lockwood and Stormont chose Coleraine specifically because it was a smaller, safer, more unionist town than Catholic-majority Derry. The decision helped fuel the civil rights movement that followed, and the same year the Stormont MP Eddie McAteer led 25,000 people on a motorcade to Stormont in protest. Magee was eventually folded into the two-campus New University of Ulster in 1969, and in 2014 became Ulster University's Derry-Londonderry campus.

Magee houses two research centres that punch above the campus's weight. The Intelligent Systems Research Centre works on neural networks, brain-computer interfacing, and cognitive robotics - it hosted the 23rd International Loebner Prize in Artificial Intelligence on 14 September 2013, the annual contest based on the Turing Test. The International Conflict Research centre, INCORE, is a joint venture with the United Nations University founded in 1993 to study conflict resolution. INCORE has hosted the Tip O'Neill Chair in Peace Studies, named for the Boston Irish-American Speaker of the US House. John Hume - Derry-born Nobel laureate and Magee alumnus - held the chair from 2002 to 2009 and used it to convene a remarkable run of guest lectures. Bill Clinton, Hillary Clinton, Kofi Annan, Bertie Ahern, Garret FitzGerald, Romano Prodi, John Kerry, and the former French Prime Minister Michel Rocard all spoke at Magee during those years. For a small campus in a small city, the visitor list reads like a UN seating chart.

Magee's graduates have scattered widely. Dill Macky, who matriculated in 1866, sailed to Sydney and founded The Scots College there, still one of Australia's leading independent schools. Mark Durkan, who served as Deputy First Minister of Northern Ireland, studied at Magee in the 1980s. Brooke Scullion, who represented Ireland at the 2022 Eurovision Song Contest with the song 'That's Rich', was at Magee in 2020. Among honorary graduates the campus has welcomed are Enya, Sir Ian McKellen, Stephen Rea, Gary Lightbody of Snow Patrol, and Paddy Ashdown. Bill Clinton received his Magee honorary degree in 1995, three years before his role in brokering the Good Friday Agreement. The campus expansion debate continues. Derry remains a city without a full-scale university of its own, and the case for growing Magee - the case that Lockwood ignored sixty years ago - has not gone away.