After being dragged under water, Doggett wakes to find himself in a nice comfy bed. He’s met by Shannon – a woman he used to be in the Marines with. She goes on to explain that she is a prototype of a super solider created during the last decade.

Meanwhile, Scully is a little freaked out by Williams new abilities and wants to learn more. Brad is getting stuck in by questioning Monica and Skinner about Doggett’s actions, which only seems to upset Monica. Meanwhile Skinner is asking Scully questions about Scully’s actions.

He states that Mulder and Scully asked Skinner to let Mulder disappear, so why is she getting involved in Doggett’s investigation? She states that something happened with William, and now she wants answers. Monica gets a break when the Lone Gunmen notice that a pay phone has been calling the dead guy from the last episode. We see the pay phone is actually a captain of a ship. He’s in command of a vessel that’s docked but has no idea what’s going on. We see some kind of lab on the ship, which even the captain isn’t allowed access to. The captain goes back to his bridge, only to find his second officer has been replaced with… Knowle!

Doggett takes Scully to see Shannon – who explains her story of super soldiers. Scully examines Shannon who claims to breathe under water, and finds nothing but an unusual spinal condition on her neck. Shannon states that they have successfully made a super solider from birth, and they plan to release the chemical into the water supply which will in turn cause pregnancies of super soldiers to be born.

Doggett gets called into Kersh’s office where Kersh and Brad explain he’s being suspended. After a few choice words between the three, Doggett basically calls their bluff and asks them to stop him before walking out. Finding out about the ship, Doggett, Monica and Scully head over to meet the captain, who spoke on the phone and states he wants to blow the lid on everything. One arriving they find Knowle… alive and well. Monica and Scully run but Doggett fires an entire round at Knowle, without hurting or slowing him down even slightly.

After a bit of a scuffle, Shannon comes out of nowhere and beheads Knowle. Counting his blessings, Doggett gets up only to see a hand shoot through Shannon, and Knowle’s decapitated body standing behind her, then the body and Shannon fall into the water. Brushing it all off, the three continue into the boat, Scully and Monica find a lab – where Scully concludes they have been doing testing on human ovum, and possibly messing with peoples DNA. Scully wants to know if she’s among the test subjects, but Doggett locates a bomb and they all make a rather dramatic exit from the fireball that was the lab. To end with, Doggett submits his investigation report to Kersh – which doesn’t mention Kersh’s name.

Doggett does as why Kersh gave him the information about the dead guy from the beginning. Kersh isn’t too open and helpful but does drop some hints that he may have helped Mulder, hence why he’s nowhere to be found – and that Scully was the one who asked Mulder to leave. It’s all a bit up in the air, and will hopefully be clearer soon.