Agent 300 is of course in his underwear because Niels stole his clothes. Hey! Maybe he was hiding gadgets!
Natalie and Duncan don’t mind the weird stalkish thing Niels is subjecting Thomas to, because Thomas is very straight and not up for any of Niels’ games.
They are however not fond of Niels flirting with Agent 300 because the guy is ridiculously mysterious about everything, so while everybody knows that he loves the ladies (especially Natalie) nobody quite knows how straight he really is, and the fact that he is flirting back is not helping matters.