The reason why the Shivans are exterminating the GTVA is because Vasudan fanatics of the Cult of Headz blew up all the tea and crumpets, because the Shivans are actually British despite the fact they aren't human.
The reason why they attacked in FS1 was because the Lucifer's crew was reading the Galactic Guide upside down, and misinterpreted the Terrans and Vasudans war as being a war on Earl Grey Tea.
See, if you managed to get rid of the Cult of Headz before they blew up all the tea and crumpets, the Shivans wouldn't be angry at us, and they would be sharing their wonderful culture with us. Thankfully, with ETAK, we should be able to tell them the next time they visit GTVA space that it was the Cult of Headz's fault that all the tea and crumpets are gone.