u/CardiologistOk909

Now for timeline confusion in episode 3x01 -

Let’s start at the “past timeline”.

The Ukrainian female agent (Elizaveta’s character) made contact with Kyle at a bar to get the CIA attention to the Russian army guy they wanted the USA to capture. Later, the QRF & Joe made contact with her on a college ground. Afterwards, the team deploys to Ukraine and the whole action sequence of the episode begins & they capture the Russian Army guy.
After they return to the USA, joe comes home at night and meets the Ukrainian/Russian dudes and shoots them on her doorstep. End of episode.

Now, for the beginning of the episode. When Joe is kidnapped, it is 6 months AFTER the Ukrainian mission. Meaning, it is also 6 months after the night incident at Joe’s house (end of 3x01).