Story's part as lead communications agency on the launch last year of M&S Bank aided the rebound in 2012.
The agency's operating profits had fallen from £628,507 in 2010 to £291,747 in 2011.
Another major piece of business for Story has been water company Highland Spring's "Full of the Joys" television advertising campaign.
Ms Mullen also highlighted Story's formation of an alliance from September 2011 with Glasgow-based agency S.O. Creative, which has brought work for the Scottish Qualifications Authority.
She also flagged Story's partnership with digital specialist The Weather, which operates out of Story's offices in Edinburgh. This alliance has enabled Story to become involved in online health-related work for the Scottish Government.
Ms Mullen said: "That is a piece of work we wouldn't have been able to tender for."
She told The Herald: "I would say that 2011 was a bit of an eye-opener for us because, up until then, we had been pretty constant, delivering constant profit in tough times."
While Story remained in the black, and turnover increased to £4.2m from £3.36m in 2010, Ms Mullen said of the fall in earnings in 2011: "It kind of made us step back, and take a really good hard look at the business.
"Through that year, it was tough month to month. It was the first time I would honestly say – and I think other people have experienced (this) a lot more – there was no visibility in the business."
Looking back at the rebound Story has enjoyed since, she added: "We have been quite canny, and strategically canny, in realising that for all of us to do well we need to choose partners, and it is mutually beneficial.
"It is interesting because that is happening as well in other sectors. It is not necessarily about mergers and acquisitions – it is about mutual working relationships.
"That is a much more positive thing for the industry to foster, because we have to support each other in what are effectively difficult times."
Ms Mullen noted that Story's higher 2012 profits had been made on turnover of about £5.1m.
She said: "2012 got us back to what I believe is a much more credible position in terms of our profit."
Ms Mullen cited the work for Marks & Spencer on the launch of its new bank as a major piece of business for Story last year.
She said: "I am really proud of that because that is a piece of business that has come to Scotland. I know we see ourselves as a UK agency but there are lots of London agencies that would have thought they might have got that."
Referring to Story's work for Highland Spring, Ms Mullen said: "That is a big achievement – to take them back on telly with a new positioning."
The agency also worked with public relations agency Weber Shandwick on communications for Serco's successful bid to run Northern Isles ferry services.
Story, which was acquired by The Mission Marketing Group in 2007 and employs 34 people, also counts HSBC's First Direct banking unit and Glenmorangie's Ardbeg among its clients.
Referring to 2011, Ms Mullen said of the view of Story's London-based parent group: "In the year we didn't do as well as we might have done, they understood it was a difficult time for the industry and they trusted the people in charge to turn it around, and that is what is so important."
Ms Mullen revealed she was budgeting for profit growth of about 10% to 15% this year.
She said: "2011 was a sobering year for us. We learned from it. I think we made the decisions we had to make so we were better placed for 2012. That proved to be the case.
"I am budgeting cautiously for 10% to 15% growth (in profit) this year, on 2012.
"The big turnaround was from 2011."
Highlighting her drive to succeed, Ms Mullen said: "My commitment is to keep the doors of Story open and to keep people employed, and to service people on the back of that.
"To do that, we have to be flexible to change and open to different ways of doing things."
She saw potential to capitalise on the "exciting time" for Scotland in 2014, with major events including the Commonwealth Games in Glasgow and the independence referendum.
Ms Mullen said: "I think the spotlight is going to be on Scotland in 2014 for all sorts of reasons. I think we need to capitalise on that, and turn that to our benefit."