The museum had two floors of interactive science exhibits, an art gallery displaying a range of works as well as a gift shop, educational classrooms and rental space for special events.

The piece, depicting a Confederate Battle Flag hanging from a wooden arm in a noose, was cited as "offensive, objectionable and tasteless" by Sons of Veterans members.

The Brogan executive director noted "There's a balance between the nature of the art that we show and the outcome that we seek, which is to promote dialogue and conversation, and have you maybe think of something in a slightly different way".

[26] The piece, “Christ Carrying the Cross Dragged by a Rogue,” by the Italian Renaissance artist Girolamo Romano, was reportedly looted from a Jewish family during the Holocaust.

In early 2013, when a bid for $150,000 in funding from Leon County fell through,[28] the museum closed permanently, with "dire financial straits" and an inability to bring in "blockbuster" exhibits cited as reasons behind the closure.

Expansion to the vacant areas can't occur until the Leon County School Board approves the terms of yet another amended lease.

"[31] By 2017, the building had been fully repurposed by TCC as non-profit innovation center: "The 34,000-square-foot facility, which formerly housed the Mary Brogan Museum of Art and Science, underwent significant renovations.

It now houses offices and conference rooms for rent, technology infused training and collaboration spaces, a retail incubator, tenants including WTXL-ABC 27 and a New Horizons Computer Learning Center, the Institute for Nonprofit Innovation and Excellence, and a Starbucks coffee shop.