“In the Flesh” is episode four of season five of Star Trek: Voyager.
At Starfleet Headquarters, Boothby, seen in the TNG episode “The First Duty”, snips a flower. An admiral welcomes three officers to the place and tells them to send any problems to his lieutenant. And someone is watching and taking pictures. That someone is Chakotay.
Chakotay is scanning some plants when Boothby approaches him, telling Chakotay that it’s bamboo. Chakotay knows but says his tricorder is saying they are maple trees. Boothby suggests going to Logistical Support; they might issue a new one. He’s going that way himself. He asks Chakotay what his assignment is. He doesn’t know; he’s arrived after a three-year tour on the Intrepid. Yes, that’s patrolling the Neutral Zone; he caught transportation at DS7. Chakotay says he’s heard of Boothby, when the latter introduces himself. Boothby hopes so as he’s been tending the grounds for 54 years. Before Chakotay leaves, Boothby warns him that Logistical Support is a secure area and won’t let him in with that holo imager. Chakotay is recording some images for friends back home. Will Boothby pose for one?
Chakotay actually heads for the officers’ club and sits, picking up a book. A woman says that’s her seat, and her book. Does Chakotay want her drink too? That depends on what it is. By the sounds of it, he wouldn’t. The woman introduces herself as Valerie Archer. Chakotay introduces himself with a false name. They chat, then something happens to one of the other officers, who is taken away. Archer asks Chakotay if he’s ever reverted, because that’s the third time this week the other has. Any more and he’ll be pulled out of training. Archer can keep human form, but has problems with the little things; breathing oxygen, bipedal locomotion, sleeping. But they shouldn’t be talking like this. Think human, talk human, be human.
Archer offers to show Chakotay around when Tuvok arrives and mentions they have work to do. Archer arranges a date with Chakotay; afterwards, Tuvok thinks that’s inadvisable. Chakotay was planning to stand her up. Tuvok says they were supposed to limit their op to surveillance. Chakotay thinks it was worth speaking to Archer; they are aliens posing as humans. Though for what purpose. They head back to the transporter coordinates, but get accosted by an Ensign Gentry. He tries bringing them in but Tuvok renders him unconscious. They take Gentry with them to the Delta Flyer. Which is near a space station, not San Francisco.
Gentry wakes up in Voyager‘s sickbay. He refuses to drop the charade when Captain Janeway tells him they know about it, giving his name, rank and serial number instead. When the Doctor tries getting a sample of Gentry’s DNA, who calls them dirty humans and kills himself.
Chakotay shows his pictures to Janeway and Seven of Nine. The simulation is incredibly accurate. Perhaps the aliens got Federation data. Or have been to San Francisco. The habitat is heavily fortified. The Doctor has something the captain will want to see. The captain is concerned this training ground could be a prelude to invasion. According to the Doctor, Gentry has been genetically altered, in a highly sophisticated way. He should be able to trigger a genetic reversion. Which he does. To Species 8472.
The captain briefs the senior staff and Tom mentions how the Soviets in the 20th century used to build replicas of American towns to train their agents. This habitat could be the same thing. Species 8472 could be planning to infiltrate the Alpha Quadrant. They may already have. Seven of Nine thinks, from previous experience, that Species 8472 may be planning to destroy Earth. Tuvok thinks that’s logical. Chakotay wants to keep his date.
Chakotay is prepping in astrometrics when Janeway joins him. She asks questions and he realises she’s testing him to see if he is still Chakotay. Chakotay understands and suggests the Doctor investigate him and Tuvok. Tuvok is already in sickbay. The captain could have just asked. Given Gentry’s reaction, Janeway though this would be more tactful. And the entire crew is going to be checked.
Seven of Nine and the Doctor are preparing new Borg nanoprobe weapons; Seven is concerned that Species 8472 may have developed a defence in the past year and is planning to make them more effective. She also points out a flaw in the Doctor’s reasoning regarding using weapons to keep the peace; several hundred million dead using nuclear weapons in World War III. Species 8472 seems to have a bad opinion of humans; they believe they are aggressive and planning an attack.