Bowser and his henchmen including his Floating Castle and Airships arrive at Pandaria.
Being Card Carrying Villains they aren’t interested in randomly starting conflict like the Alliance and Horde. Of course they get the idea to have Bowser Jr. take the form of Shadow Mario unleashing Graffiti just in case Mario shows up.
Being utterly assured of Mario coming in to clean the place up Bowser has his recon troops assess the situation upon which they discover the Alliance & Horde fighting and unleashing the Sha.
Bowser loves the Sha’s unique power and has his Henchmen gather as many Sha as possible and stuff them into containers while making preparations for Kamek and the Koopa Troop to unleash the Sha upon both Stormwind and Orgrimmar.
Thanks to Kamek enlarging the Containers holding the Sha the corruption of Stormwind via hosing it with Sha is a success and Elwynn Forest, Westfall, Duskwood and Redridge Mountains are all corrupted heavily by the Sha Energies of Doubt!
Durotar, Northern Barrens and Azshara are also hosed with Sha Corruption and are reduced to ruin!
The Alliance and Horde are completely caught off-guard by the Weapon’s test of an outside faction seeing them as target practice! Furthermore there are no survivors from the attacked territories informing the rest of the territories of who caused this mysterious attack which is naturally blamed on the opposing Faction.
Bowser promptly hoses the Mushroom Kingdom and devastates it as he makes off with Princess Peach. The Toads as usual are defenseless against the Koopa Kingdom’s attack even as the Sha Corruption causes more damage than usual(which considering Kamek turned the Princess Peach’s Castle into a Lava-filled fortress in one game while Bowser once bombarded it with Cannonballs in another is saying something).
Bowser gets beaten by Mario who rescues Princess Peach returning her to the now Sha-Ravaged Mushroom Kingdom.
Bowser of course returns to the drawing board analyzing Pandaria some more and quickly discovers first the Mogu Statues being animated by Ghosts and the Alementals as well as the Waters of Youth and has his Henchmen grab a few of the Alementals as well as the Waters of Youth which are placed in bottles.
Then Bowser tests out the Alementals on Khaz Modan and Lordaeron drowning both in a torrent of Mountain-sized Alementals. Then Bowser uses the Magically-increased size Tanks containing the Waters of Youth to kill Teldrassil, Darkshore, Ashenvale, Dustwallow Marsh & Mulgore while turning the South Barrens and Thousand Needles into sprawling out of control Jungles choking out all inhabitants!
Satisfied he unleashes both on the Mushroom Kingdom and kidnaps Princess Peach. Mario rescues Peach and returns her to a now completely dead Sha infested Wasteland flooded with Ale.
Peach is forced to move the Mushroom Kingdom away as Bowser continues his study of Pandaria and discovers the Will of the Emperor as well as the Mantid.
He promptly steals the Egg of the new potential Mantid Queen(after stomping flat the old one), the Kypari Trees and the Will of the Emperor for himself. He also learns the techniques of Fleshshaping and uses it to enhance his Armies. He furthermore uncovers the Divine Bell and the Heart of Y’Shaarj.
He takes the Heart to the Divine Pools and since Taran Zhu had gotten wind of this tries to intervene before Bowser beats him up and throws the Heart into the Pools to revive it in an act of Arrogance unleashing a Sha of Pride outbreak.
He later consumes the Heart like Garrosh does and gets a power boost while continuing his invasion of the Mushroom Kingdom as usual.