It's years after the events of the first film and Alice Kingsleigh is the captain of a merchant ship. When we first see her she's evading pirate ships during a stop and barely gets away. It's clear she loves adventure, so when she finds out that her ex-fiancee has purchased her ship (to cover her mother's debts on the house), she's dismayed. She so upset that this allows her to go back to Wonderland. Things aren't much better there. The "Mad Hatter" (Johnny Depp) is in a bad way. He's found a relic from his past and is convinced his family, thought to be killed by the Jaberwocky years ago, is alive. Only no one believes him and it has made him serious and bitter. Alice is dismayed to see her old friend like this wants to help, so she visits the personification of Time (Sacha baron Cohen) and steals the chronosphere, which is basically a time travel device that navigates the sea of time. Alice ends up going back in time, several times, and we learn the origins off everyone from The Mad Hatter to Iracebeth, The Queen of Hearts, and how she got that enormous noggin. This second film is both a sequel and a prequel.
This is a much better movie than the Tim Burton original and one in which the CGI effects are really the star.