After Fran Rooney's departure subsequent management teams sold off the different business units that had been developed over the years in a series of demergers and by December 2003, following the sale of the PKI business to Betrusted, the company had shed all operating businesses. In March 2004 the board announced its intention to move into the clean energy space, starting with an acquisition, though no acquisition target was ever publicly identified. The plan was abandoned in June 2004 and the company was acquired by Acquisitor Holdings of Bermuda in July 2004 following some acrimony between Acquisitor and Baltimore management. In February 2005 Acquisitor delisted Baltimore from the FTSE.
The company listed on the UK Alternative Investment Market at the end of February 2006 under the symbol BLM. In May 2006, the company released an AGM Statement (PDF) which describes the company's strategy as "becoming a financial services business concentrating on those specialist areas of the market where we have the skills and track record to obtain an operational multiple on the valuation of our shares." The statement lists companies that Baltimore Technologies has bought and sold, implying a strategy of investing in undervalued small companies.
Sarah Flannery won the European Young Scientist of the Year award for her presentation of the Cayley-Purser algorithm, which was based on work she performed with Baltimore researchers during a short internship with the company. The algorithm is named after Michael Purser.