In the Flesh ( episode ) " Voyager " finds a station containing a disturbingly accurate re - creation of Starfleet Command and Starfleet Academy by Species 8472 . Summary . Teaser . In what is seemingly San Francisco on Earth , in the grounds of Starfleet Academy , an old man tends some flower s . About him , bright young Starfleet cadet s walk to and fro . The sky is bright and sunny ; a perfect day . A distinguished looking Starfleet admiral addresses a group of just graduated and commission ed officer s . In a no - nonsense tone , the admiral introduces himself as Admiral Bullock . He welcomes them to Earth and invites them to direct any questions or comments they have to him . Any problems are to be directed to Lieutenant Kinis , the admiral ' s Vulcan aide standing next to the admiral . From afar , an officer is seen to be watching them using a holo - imager and taking pictures . It is revealed to be the ' s first officer , Commander Chakotay . Act One . Chakotay is taking some scans when the same old man who was tending the flowers comes up behind him , jokes that his tricorder scans are unnecessary , and identifies the plants . Chakotay chuckles , and smoothly responds that his tricorder is malfunctioning . The old man introduces himself as . Boothby asks him about his posting . Chakotay makes up a story about being assigned to the patrolling the Romulan Neutral Zone . Boothby advises him to get a new tricorder from Logistical Support . He is on the way to that area himself . Before they start off , Chakotay makes sure to get an image of him . Chakotay enters the officers ' club , the Quantum Café , sits in an empty seat and thumbs through a book . A Human female commander approaches him and introduces herself as Valerie Archer . They sit and talk amicably when suddenly an officer sitting in a corner begins gagging and spasming in agony . Strangely enough , no one seems alarmed ; two officers just drag him away and that is all . Archer turns back to Chakotay and tensely asks him if he has ever reverted . He responds nonchalantly , not yet . She identifies the officer as Ensign O ' Halloran , and comments that he will be pulled out of training if this happens to him again . She states that she can keep her Human form , but complains about things she has to put up with in that form such as sleep ing , breathing oxygen and bipedal locomotion . Chakotay merely smiles . He then tells her that he is new , and she makes a date with him that evening to show him around . Lt . Commander Tuvok approaches them and politely tells Chakotay that they have to leave . After the two " Voyager " officers get out of earshot , Chakotay tells him he has gained useful information about what is happening here . They leave the club , heading to prearranged transporter coordinates . Suddenly an ensign accosts them , telling them they are in a restricted area and need to accompany him . They refuse , and when the ensign insists , Tuvok drops him with a Vulcan nerve pinch . They catch him as he falls and Chakotay taps his combadge to be beamed back to the " Delta Flyer " piloted by Tom Paris . The " Flyer " turns and leaves orbit , not around Earth , but an alien space station . Act Two . The ensign wakes up to find himself in " Voyager " s sickbay , agitatedly asking where he is . He begins to act angry , threatening to report his abduction to " the admiral " . Janeway impatiently tells him to cut the act : they know he is not Human . She demands his identity . He identifies himself as David Gentry , rank ensign , serial number : 99 - Beta - 3278 , planet of origin : Earth . Janeway coldly responds that they are not interested in his knowledge of Human culture and that they are not part of his re - creation . The petrified ensign repeats his POW - style self - identification , maintaining that Earth is his homeworld . When Janeway realizes that she is obviously not going to get any answers out of him , she asks The Doctor to take a genetic sample from him . The ensign desperately taps his combadge , to no avail and then suddenly springs off the bio - bed and backs against a wall , screaming . His head snaps back and he collapses . According to The Doctor , he has released a cellular toxin into his bloodstream and is dead . In astrometrics , Chakotay and Tuvok show Janeway and the other senior officers the images that Chakotay has taken , and report on what they have learned . These aliens , whoever and whatever they are , have carefully reconstructed not just Starfleet Academy , but the entire Starfleet Command complex . Seven of Nine reports that she has determined the nature of the alien station : it is essentially a huge holographic facility . The Doctor hails Janeway and reports that he is ready to begin his autopsy of the alien . Before she leaves to go to sickbay , she orders them to search for any tactical vulnerabilities the station may have . In sickbay , The Doctor informs Janeway that the alien is most definitely not Human . It has been altered genetically on an extremely sophisticated level and only micro - cellular scans could distinguish it from a real Human . When he administers a cytokinetic injection to reverse the process , it is revealed to be Species 8472 . Janeway immediately calls a meeting of her senior staff and informs them of the aliens ' identity . They now have no doubt the re - creation is for sinister motives . Species 8472 had made their intention to purge their galaxy of all life very clear . Now , they have re - created Starfleet Command and are training to pose as Starfleet officers . The whole thing reeks of preparation for invasion - possibly of Earth . Janeway orders Tuvok to continue searching for a tactical weakness in the station , and orders Seven to immediately begin re - manufacturing the modified Borg nanoprobe s , in large numbers . Chakotay decides to keep his date with Archer , since he could get more information out of her . Janeway agrees , and then reminds everyone of the importance of their success ; Starfleet has no way of stopping Species 8472 , nor can " Voyager " ' s crew warn them of the invasion . Act Three . Captain Janeway orders the entire crew to report to The Doctor for DNA testing , to ensure that no impostor is aboard . The Doctor certifies Chakotay and Tuvok respectively as genuinely Human and Vulcan . With that settled , Chakotay goes off to keep his date with " Commander Valerie Archer " . He , Lt . Paris and Ensign Kim return to the facility on the " Delta Flyer " . They arrive , remaining beyond sensor range , but within transporter range , and Chakotay beams in . In " Voyager " s sickbay , Seven and The Doctor observe the newly - manufactured modified Borg nanoprobes . She has taken the precaution of increasing their mobility and efficiency in case the aliens developed a defense against them in over a year since their first encounter . While The Doctor hopes they will be able to solve this through more diplomatic channels , Seven merely scoffs at the idea that Species 8472 would even acknowledge the concept of diplomacy . It is " night " in the re - creation . Chakotay enters the " Quantum Cafe " and finds " Archer " sitting at a table with " Boothby " . " Boothby " takes his leave and Chakotay sits with " Archer " . They decide to go dancing . Sometime later , they return to her quarters . The date has apparently gone well . The conversation turns to Humans . She marvels at the ability of " such a violent species " to create so many beautiful ways to express their ideas through art , music , literature and so on . But , she insists , they are dangerous , quick to attack any species that is not part of their Federation . After a while she feels the need for an isomorphic injection to preserve her Human form , so she excuses herself and leaves the room . While she is gone , Chakotay goes to her computer terminal and downloads all data in it . Chakotay ' s attempts to try and introduce doubt about her perception of Humans fail , as she insists their threat is grave . He drops the subject , not wanting to push too much and possibly arouse suspicion . He excuses himself , telling her he has a tactical report to finish for the next morning . However , before he leaves , she touches his face and kisses him , saying that Human dating rituals are part of their training . Initially somewhat reluctant he finally caves in . After he leaves , she takes scans of her skin that touched Chakotay ' s and immediately contacts " Boothby " ; Chakotay ' s cover has been blown wide open . He asks her how much she thinks he knows . She cannot say , but recommends his capture and interrogation . Chakotay is walking past an ornamental lake when the sky instantly shifts from dark night to bright day . He looks around , startled , to see he is being followed . Worse , along all the paths , several of the aliens in their ersatz forms are converging on him . Realizing immediately his cover is no more , he tries to hail the " Flyer " , but gets no response and is finally captured . Act Four . Captain Janeway is in her ready room with Seven and clearly conflicted over something . Starfleet Directive 010 , she tells Seven , mandates that any and all attempts at diplomatic resolution must be made before engaging an alien species in battle . In Species 8472 ' s case , they did that and barely survived . Military engagement therefore appears to be the only course of action . Yet , Janeway cannot get this directive out of her mind . Tuvok calls her to the bridge , where she is informed of having lost contact with Chakotay and that he cannot transport back . Janeway orders red alert and the nanoprobe torpedoes brought online . Chakotay is interrogated by " Boothby " in the empty " Quantum Cafe " . He demands to know how they found them . Chakotay responds that it was due to the detection of what appeared to be a Federation frequency . Of course , they tracked its source . " Boothby " demands other information about their planned attack , but Chakotay insists that a war is not being planned against them . " Admiral Bullock " enters . He acts deferentially toward " Boothby " , indicating that this alien is , in fact , the operation ' s commander . He informs " Boothby " of " Voyager " s approach . " Boothby " orders battle stations , ignoring Chakotay ' s insistence that Captain Janeway is coming only to retrieve him , not attack . Janeway orders " Voyager " brought into weapons range , and orders Seven , at the auxiliary tactical station , to target the facility ' s weapons array . Seven suggests that its power systems be targeted as well . But , even on the brink of hostilities , Janeway looks for a way to avoid casualties , if not belligerence altogether . She does not want to risk harming the aliens ' life support . Seven insists that they are undeserving of compassion . Janeway sharply responds that this is not the time for an ethical debate and angrily repeats the order . A hail comes through : " Boothby " greets her cordially . She sarcastically asks him if he is enjoying the Delta Quadrant . In response , he snaps that the weapons at his disposal allow him to destroy " Voyager " with but a single command . He asks her to retreat . Janeway , of course , refuses to go anywhere until he returns her first officer and provides a good explanation as to why they are again in the Milky Way . She informs him of the weapons she has trained on them ; weapons whose potency against them he is well aware of , reminding him of the heavy casualties his species suffered the last time they engaged each other . She comments that an armed conflict is not going to solve their problems and proposes a meeting . Act Five . In " Voyager " s briefing room , representatives of the two sides are gathered . " Boothby " angrily denounces the Federation and its values of tolerance for all species and the Prime Directive as " targ manure " . Janeway insists that the Federation adheres to its directives . " Bullock " counters that her actions say differently , and accuses them of infiltrating their re - creation , capturing and killing one of their people . " Bullock " angrily continues , further accusing them of creating biological weapons to use against them , and being allies of the Borg . Janeway denies all charges , stating that Seven is no longer part of the Borg collective . She tries to convince " Boothby " that the Federation is not set out to get or destroy them , but when the aliens keep questioning each and every one of her points , Janeway soon realizes that this is getting nowhere . She asserts that there is only one way to prove that they speak the truth , namely trusting each other . She then orders Seven to disarm the nanoprobe warheads to prove their point . She calmly responds that one of them has to take their finger off the trigger and that she will be the one . " Boothby " is struck by her action . He agrees to continue , but insists that they get to the issues that are the bones of contention . Janeway explains that , far from informing Starfleet about them , " Voyager " is , in fact , alone in the quadrant and has not had any contact with the Federation for the past four years . She explains that at the time they engaged Species 8472 , they were unaware that the Borg had started the war against them and were acting in self defense . " Bullock " , unimpressed by Janeway ' s standing down of " Voyager " s weapons , urges " Boothby " to say nothing . " Archer " , however , has been won over and informs the Starfleet side that their mission is solely reconnaissance . " Bullock " still insists that they should not negotiate with them . " Boothby " orders him to return to his seat . " Archer " stands her ground . She tells them that after seeing through Human eyes , she now wonders as to the veracity of their belief of the Humans ' violent nature . " Bullock " insists that they cannot risk trusting them . She retorts by demanding of him if he would rather risk another war . After a long discussion , " Boothby " is finally ready to go along , but insists some pre - conditions must be met , namely she must grant them access to the modified nanoprobe technology to study it . Janeway agrees , in return for access to the genetic manipulation techniques they use for appearing Human . The spirit of détente has been created . Seven is not at all convinced that this diplomatic dealing will work . Janeway exhorts her to have a little faith and asks her if she wants to come to the facility ; it would be her first look at Earth . Seven declines ; she prefers to stay aboard in case any problems arise . Janeway confidently assures her there will be none . On the grounds of the Starfleet Command recreation , " Bullock " and " Kinis " are standing alongside Tuvok and Neelix . In a manner similar to the training scenario , " Bullock " introduces himself and welcomes Tuvok and Neelix to " Terrasphere 8 , Starfleet Command re - creation " . As in the training scenario before , he invites them to direct any questions or comments they have to him , and problems to " Kinis " . Tuvok and Neelix are here to see some of the facility ' s technology . " Bullock " addresses Neelix as " Ambassador Nelix " , mispronouncing Neelix ' s name , and is quickly corrected . Janeway and " Boothby " walk along a path , talking . He welcomes them to stay for a while as they will not be returning to fluidic space for a few days yet , but she declines , saying she would like to get back on course for the real Earth . As they stop at a fence by an ornamental lake , she asks him concernedly about the chances of him being listened to . He responds that he cannot promise anything but that he will tell them what has happened , and perhaps that will win some of them over . Janeway expresses hope that the process will lead to full diplomatic relations between their species . He has " Voyager " s com frequency , should he need to contact them . As a final gesture , " Boothby " gives her a large , lovely , genetically - engineered rose , just like the ones the real Boothby used to give her . Chakotay and " Archer " walk together one last time . She tells him she is looking forward to returning home to fluidic space and resuming her true form . He compliments her on making a terrific Human , and she offers to give him a tour of their realm sometime . Before parting , she kisses him again telling him that this attempt was better . " Voyager " is seen pulling away from the station , resuming course for home . Memorable quotes . " " Don ' t get sassy with me , young lady ! This re - creation may be Starfleet but our weapons are far more sophisticated . I can destroy your vessel with a single command . Run along , now . " " " Targ manure ! " ' United Federation of Planets ' . . . ' tolerance for all species ' . . . the ' Prime Directive ' . . . " targ manure " , every " word " of it ! " " " " Humans ! You ' ve got a flair for the dramatic , I ' ll give you that . You want to keep talking ? Fine by me . But no more beating around the bush ! Now what do you want from us ? The truth , captain ! " " " " Once a Borg . . . " always " a Borg . " " " " First of all , I want to take a look at that nanoprobe technology - it scares the hell out of me ! " " " " Voyager " may be the last defense against an all - out invasion of Earth . " " " " Just be home before midnight . " " " " I ' ve always wondered what it would be like to date an alien . " " " " I ' ll take notes . " " " " There are no secrets except the secrets that keep themselves . " " Links and references . References . 21st century ; 2368 ; " " ; Alpha Quadrant ; Archer ' s parents ; astrometrics ; Astrophysics ; Badlands ; bamboo ; " Beyond the Galactic Edge , Humanity ' s Quest for Infinity " ; bioscan ; bloodwine ; Bolian sector ; bookshelf ; Boothby ; Bullock ; capillary scan ; cellular toxin ; chopstick ; class 3 moon ; class 10 photon torpedo ; class reunion ; coffee shop ; colorful metaphor ; ; cytokinetic injection ; dash ; debate ; Deep Space 7 ; " Delta Flyer " ; Delta Quadrant ; Directive 010 ; DNA ; double agent ; Earth ; edition ; Embarcadero ; epidermal neural receptor ; ethics ; ; Federation ; Federation Council ; Federation database ; Ferengi ; field commission ; fluidic space ; " gagh " ; ; genetic extraction ; ; gin ; ; Hesterman ; hologram ; holo - imager ; " Hor ' Cha " , IKS ; Interspecies Ethics ; ; isodyne relay ; isomorphic injection ; Japanese ; kilometer ; Kinis ; kiss ; Klingon ; Klingon martini ; Larsen ; ; logic ; Logistical Support ; ; manure ; maple tree ; Maquis ; Market Street ; microcellular scan ; midnight orchid ; Milky Way Galaxy ; nanoprobe s ; Night Owl ; Namimby ; ; O ' Halloran ; Orbital Flight Control ; paranoid ; particle synthesis ; pattern buffer ; Petri dish ; ; " pon farr " ; postmortem analysis ; Quantum Café ; red alert ; Reiskin ; replimat ; resumé ; ; Romulan ; Romulan Neutral Zone ; San Francisco ; service number ; ; sheep ; single malt ; Soviet Union ; Species 8472 ; Starfleet Academy ; Starfleet database ; Starfleet Intelligence ; Starfleet Medical ; suicide ; tactical alert ; Tactical Analysis ; targ ; teetotaler ; Terrasphere 8 ; the real McCoy ; thermionic generator ; toast ; transoptic datalink ; tricorder ; type 1 phaser ; vermouth ; Vulcan s ; Vulcan nerve pinch ; Vulcan nightclub ; wolf ; World War III ; yellow alert ; Young