Hi, piscean. I'm sorry not to have responded before. I normally drop by daily but the site was down for maintenance yesterday, so I missed your post.
I'm assuming you left the cave, with the bushes covering the obvious exit, via the opening at the top and found the barracks and bunker across the viaduct. No, you don't have to go back through the closed entrance. Just make your way down the hillside and you "rejoin" the game but with some extra goodies
It's a while now since I did the final boss fight, so I'll tell you what I remember but I'd be pleased if anyone could correct me if I've got it wrong. Although everything is crumbling around you, you can still get up to a number of ledges around the area. Get above the Beast and you're safe from its attack. Chuck everything you've got at it. See the "David & Goliath" Challenge Room vid on the NVN Guide site to see how effective this is. If the ledge crumbles, run like mad to the next and repeat. There's no "trick" to killing it. Just blast it for long enough.
I hope that helps. If you're still stuck, let me know and I'll replay the chapter to jog my memory.
Good luck.