I suspect the C.A.T.T found them right when Lorem's about to deliver and they're forced to go their own way (Zeke being decoy or something so Lorem can escape), that's why Zeke ends up working for C.A.T.T again and Lorem doesn't harbor any bad feelings for Zeke, even saying he helped them (Lorem...
I don't think the writer wrote this with cuteness/lighthearted in mind. It's seinen alright, the comedy and the art being cute is for the purpose of irony, I guess. It makes me thinking "there are people like this out there huh". Wondering what she'll do next and the reaction of people around...