After defeating Giant False Ridley and reviving the real one. Ridley then proceeded to explain what had happened, but couldn't as the configuration of his vocal cords made speaking English incredibly difficult. Mewtwo, who is telepathic, volunteers himself as a translator.
The explanation goes that after the events of "The Great Maze", Ridley, Petey Piranha and Porky Minch became trapped in subspace. For an unknown time(which just happens to be a year), the three of them were trapped until a group of explorers ventured into subspace with what appeared to be Shadow Lugia as a captive. The three of them investigated these explorers and found they were comprised of Ganondorf, Protoman, King K. Rool, Metal Sonic, Black Shadow, Dr. Eggman and the Shake King(see Wario Land Shake It!). It seems that they were quite impressed by Tabuu's power and each sought to use them for their own purposes.
They decided to join together and see if a piece of Tabuu still existed. Dr. Eggman uses Shadow Lugia as a power source for his own subspace portal(which is why Shadow Lugia appeared as a captive). They soon found Tabuu's heart, their plan was to clone him from the DNA in his heart and siphon off the power from his form. As they were leaving subspace, the heart began to spasm and dissolve, they soon discovered that like Tabuu himself, no piece of him could leave subspace. They decided to clone Tabuu in subspace, but their machine had the unexpected effect of reviving him instead of cloning him.
Tabuu then tried to tempt them with promises of money and power in exchange for their service, but only Dr. Eggman(who secretly plotted to betray him and take over the world using his power) and the Shake King(who was just in it for the money) Tabuu then proceeded to turn all those who resisted into trophies when Petey Piranha and Porky Minch pleaded to rejoin Tabuu's ranks, but Ridley refused and was turned into a trophy along with Ganondorf, Metal Sonic, Protoman, King K. Rool and Black Shadow. Eventually, Tabuu discovered that by combining his powers with those of Shadow Lugia, he could produce an endless army of Shadow Bugs and allow them to take the form of pokemon. He could also tear holes in the fabric of space and time and into other dimensions, which is how he disposed of all the trophified characters with the exception of Ridley.
After this explanation, you have the rest of the level, which thankfully isn't that long. After you complete the level, everyone from Group B joins your party(so does Ridley if you went through the door and defeated his giant doppleganger).
Group B must now travel through space and time and into parallel universes to rescue everyone.