As you've probably noticed the roots are still here, so you'll be forced to head through a short tunnel. Use the hook to grapple up to a small opening (screenshot #1) and continue with your approach. Be careful, because all the plants found in the building will be releasing three orbs instead of two. Having a Triple Batarang ability really helps, because otherwise you'll have to be very fast in order to avoid any injuries.
Keep moving forward until you'll get to a door leading to the Botanical Glasshouse. Once you're inside you'll have to get rid of a new set of plants. Focus on finding the door leading to the Flooded Corridor (screenshot #1). You'll have to use the Line Launcher here to reach the other side of the pool safely. Once you've landed destroy the glowing spheres and then a new plant.
Notice than Poison Ivy has unlocked the main corridor for you, so you won't have to go through the side room to get to the northern section of the building. Keep heading forward until you encounter two guards. They're the same ones you've rescued before, but in the meantime Ivy has taken control over them. Thankfully defeating them is very easy and can be done without any health losses.
Knock out both guards and proceed to your left. You'll end standing near a large gap again (screenshot #1), so you'll have to use the Line Launcher to cross to the other side. Head on to your right and open the door to find yourself in Elizabeth Arkham Glasshouse. Get ready for a challenging boss battle with Poison Ivy!
This battle will be split into two parts, however the first part will be much easier. Each part will also consist of two phases and they will be starting alternately. The first phase will require you to remain on the move while Poison Ivy will try to catch you with her roots. When you notice the plants appearing near Batman leave that area immediately before you're caught. If you fail you won't die right away, however you will lose some health trying to free yourself.
Ivy's roots will be appearing in one of three spots - in the left section of the arena, in the middle and in the right section. You must keep moving until you'll automatically advance to phase two. In this case you'll also be running a lot, however Ivy will begin firing red orbs at you. Each hit can take a lot of your health points, so obviously you'll have to focus on staying alive.
During the second phase you'll have to wait for Ivy to reveal herself for a short period of time. Once you see her inside the large plant throw a quick Batarang at her (the one without having to aim manually). Ivy will be hit and she'll lose a lot of health points. Notice that you've made her angry and you'll have to avoid more orbs being fired at you.
Keep repeating all the actions mentioned above, constantly switching between both phases. You'll have to wait for Ivy's health bar to be drained completely. Notice that the large plant has fallen. Approach Ivy quickly and use the Explosive Gel to plant a device on her. The rest will happen automatically. Once you've witnessed a cut-scene you'll advance to the second part of this battle. Thankfully the game will create a checkpoint here, so if you fail from now on you won't have to start from the beginning.
The biggest difference in the second part of the battle is that you'll have to keep defending yourself against Ivy's thugs each time you've advanced to the first phase. Obviously this will make matters worse. Avoid using complex combos, because you'll have to focus on avoiding Ivy's roots at the same time. Instead keep running and throwing single punches.
You can use a trick to help you in staying alive. Notice that if you attack enemies standing close to the abyss they'll lose balance and fall. Having all the abilities which improve Batman's fighting skills may also prove to be useful. You should know that each second phase will remain the same, so you'll have to wait for Ivy to reveal herself and avoid the fireballs.
Just as before you must drain Ivy's healthbar before you'll be allowed to finish her off (for good this time). Choose the explosive gel and approach the boss. This time Ivy's plant won't return to life. Watch a new cut-scene after which you'll end up in Arkham North.