Alright, I would love to tell you to go and watch s5 right now... So I will. I'm assuming what happened is that you were disheartened with what happened in s4 and simply didn't want to suffer through another terrible (and, now, Cordelia-less) season of Angel. Fortunately, you wont have to. Although I personally like season 1 and 2 more that 5, it is still an incredible season. So go watch it.
HOWEVER, since you're question was not "should I watch s5 of Angel?" but rather, "can someone explain the last episode?" I'm not just gonna preach. I'm assuming you're confused about who it is that Angel and his gang were so keen on killing and why. Thankfully for you, season 5 of Angel was kinda rushed at the end, so it was ALL explained in the episode Power Play. Basically, the Senior Partners of Wolfram and Heart (you'll remember them from every other story arch) have a group of representatives on Earth. They are known as the Circle of the Black Thorn. They run things for the senior partners, and they are all very much evil. They are the people that Angel is trying to kill. Why? Because he's realized that there is nothing else he can do. He's spent the last year working at Wolfram and Heart, and he's only been achieving minor amounts of good. He decided that the only way to really hurt the Senior Partners was to kill the Circle of the Black Thorn.
Another, part of the story arch is that in the last few episodes of the season Angel had seemed as though he was turning evil. In fact, it is made pretty clear that Angel had been trying to get INTO the Circle of the Black Thorn, thus becoming completely evil. There was even an insinuation that Angel had planned Fred's death in order to get in. At the end of Power Play, Angel explains that all of these 'theories' were part of a scheme. He did, in fact, get into the Circle of the Black Thorn; but he did so because he wanted to kill them from the inside.
Finally, you might be wondering who it is that Angel had that epic final battle with. That would be Marcus Hamilton (played by Adam Baldwin). He is a representative of the Senior Partners that had been keeping tabs on Angel since ep. 17 (before that it was a woman called Eve).
I think that covers it all. You should still watch s5, but in case you aren't going to, at least you'll be able to understand the finale.