Sorry for taking so long to respond, and for misremembering my previous "advice", I've since gone back and replayed that section of the game to refresh my memory.
There are three town maps, with the hotel on the third one. You may already know this, especially if you were trying to complete Thompson's miniquest to retrieve the lost soldiers, but on the second of the three town maps there's a two-story building you can go into. On the second floor of that building, destroy the unique-looking plant in the southeast section by shooting it, and you'll then be able to proceed into an overgrown area to the north (along with all the plants inside the house and on the second town map dying). In that area, go up and investigate the female soldier - you'll need bleach to free her. After getting her out, either automatically or by investigating the spot where she was held you should get something called a Plant Heart. These can be acquired by investigating female captives of the plants, and need to be used to open up the pulsating red blockades.
For the rest of the area, I remember it being relatively straightforward - just stop at each pulsating red wall and investigate any other routes until you get a plant heart. If you don't have like 5-6 things of bleach, you might want to go back to the military base and buy some, but probably you should be good.