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It's up to you to figure it out, or you can do a full pacifist route to directly get the answer. I've already given away enough info as it is.

Can you both please cool off with the insult hurling comments? This is already a ridiculously long chain of messages that serve no purpose other than egg you both on and bloat the game's page.

For Section 1 you need to empty all encounters in the areas before you encounter Napstablook. For Blooky you need to do a certain ACT with Susie to continue, and once done you empty the rest of the encounters before entering Toriel’s guest bedroom. You know you’re done with Section 1 when an ominous message pops up and the music becomes gloomy. Kill Flowey and that’s it for S1.

For Section 2 the place you start off can be a long tolling one. You need to backtrack to hunt every enemy in the Valleys before you encounter the snake. This is an attempt to discourage your murders but if you succeed, you’ll get an ominous message and music change.

The Snake is free to kill now. Thankfully you only need to kill each enemy once by this point. Once you’re at the village you should still go to Paula. She won’t join you, but you’ll get the Franklin Badge so you can fight the cult leader yourself. When done with the leader, you now need to hunt every enemy in the cave before fighting Mondo Mole. Once past Mondo Mole, the genocide for S2 is fully locked in.

Paula joining you means you failed the genocide run at some point and are back on neutral. If you heard a happy-sounding jingle, it marks the point where it failed.
You may kill like in UT, but you need to hunt down every overworld enemy available like in DR. There's 3 times you need to kill each enemy, and they respawn when you exit and re-enter the room. This applies to both Section 1 and Section 2.
I feel like you may have failed on S2's Valley area, but it's just a guess.