The MC has a way of ending his political rivals, both at home and abroad, in rather convoluted and terrifying ways. It almost makes me wonder how much of this empress being nice to him is because she's a legitimately nice person who likes him (though this is contradicted by her own sister saying how the empress avoids all close relationships outside of their family) and how much of her niceness is to avoid her nation becoming one of Souma's eventual targets. As much as it would be best if it were the latter, I've read enough manga to know that it's really the former.