You may now enter the elevator, and interacting with the panel inside will take you to the lower level where the boss fight is. By this point you should be prepared with good weapons and perks, shields, a gas mask, and someone with the Masamune.
Using the Masamune, shoot some orange spores out of your path to get into the room.
To start the fight, shoot one of the four arms that has a glowing orange spore with the Masamune.
Many Thrashers and spiders will spawn. Start running around, killing as many as you can, avoiding the arms as they slam to the ground. Occasionally after killing enough Thrashers a max ammo will spawn in the middle of the room.
Once one of the arms of the boss has a glowing orange spot, shoot it with the Masamune to damage Takeo.
Repeat this two more times and the fight will be over. The trickiest part is simply surviving long enough until the orange spores are revealed. The cutscene should then play and you will have completed Seeds of Doubt.