Mickey's Taliban Adventures is one of almost 300 pieces in the Royal Scottish Academy's student exhibition in Edinburgh, which opened to the public on Saturday.
The exhibition by final-year and postgraduate students from Scotland's art and architectural schools also includes a short film showing the dying moments of a poisoned mouse.
The Twin Towers work - based on the attack on New York on 11 September 2001 in which 2752 people died - was made by Alan Bennie of the Edinburgh College of Art.
It shows the Disney figurehead flying a toy plane into cartoon-like foam models of the World Trade Centre, which have been given eyes to lend them a surprised expression, as well as flames made of felt.
"I don't think it's a particularly shocking piece," said Colin Greenslade, exhibitions co-ordinator for the Royal Scottish Academy.
"The Twin Towers have become an icon and everyone has their own feelings about it, whether they knew people who were involved or can just remember where they were when it happened," he said.
"This is about making you think."
The film of the poisoned mouse, by student Jock Mooney, is exhibited next to a statement explaining the circumstances, following complaints from animal rights activists.
In it, Mooney said the mouse had already been poisoned when he found it outside his flat and that his film was intended to show the effects of the methods used to get rid of rodents.