Three years after the events of the previous film, Commander Patrick Ross leads a manned mission to Mars. Soil samples collected by Patrick's team of astronauts unwittingly contain an extraterrestrial substance which thaws aboard their capsule due to the temperature difference and contaminates them, causing a seven-minute contact gap with mission control. With seemingly no subsequent negative effects, the astronauts return to Earth to public celebration. Only an institutionalized former scientist, Dr. Cromwell, reacts to their return with violent panic. Meanwhile, Dr. Laura Baker has created a clone of Sil named Eve, whose alien DNA is suppressed to make her more docile. Her team conducts experiments on Eve, hoping to find a way to combat the alien species should it ever return to Earth. Every experiment is unsuccessful as Eve's biology adapts.
Upon their return, Patrick and his team are told to refrain from sexual activity for ten days. Patrick disregards this advice and has a threesome with two sisters following a fundraiser. During intercourse with the second woman, he begins to sprout tentacles. The lady notices his transformation while she is stroking his body and is horrified at the sight of him whereupon she tries to free herself from his clutches. Both mothers experience accelerated pregnancies, culminating when Patrick's half-alien children tear out of their abdomens. Patrick hides both corpses and his rapidly growing sons on the property of his father, U.S. Senator Judson Ross. The next day, Patrick tells his father he cannot remember the previous night's events. Senator Ross indicates that he is aware of Patrick's behavior and tells him to focus on his political goals.
Dr. Orinsky, one of the NASA scientists who examined Patrick, discovers something amiss about his blood sample and desperately tries to contact Cromwell. However, Orinsky is ambushed and disemboweled by an alien Patrick, who snuck into the labs. Laura discovers that the DNA in Orinsky's wounds is distinct from Eve's, prompting Colonel Burgess, the military supervisor in charge of her project, to reunite her with Press Lennox to contain the new threat. Press and Laura seek out Cromwell, Orinsky's former professor, and learn that he discovered that the alien species had attacked and destroyed Mars in ancient times. Because of his fears that alien DNA might remain on Mars to infect anyone who visited the planet in the future, Cromwell urged the government to abort the mission, but was institutionalized to permanently silence him.
Press and Laura report their findings to Burgess, identifying the Mars astronauts as the prime suspects. Unable to find Patrick, they pursue the other astronauts, Anne Sampas and Dennis Gamble. They arrive too late to prevent Anne from having sex with her husband, resulting in her impregnation with hybrid offspring. The tentacle-like creature bursts from Anne's abdomen and kills her husband before Press and Laura manage to kill it; Anne dies of her injuries. Meanwhile, a second team of government agents locate and examine the third astronaut, Dennis Gamble, but confirm he is not infected. Laura discovers that Anne's hybrid DNA does not match that in Orinsky's wounds, meaning Patrick is the killer. Meanwhile, Patrick has sex with his fiancée, resulting in her death and the birth of another hybrid son. Patrick attempts suicide by shotgun, but the alien DNA regenerates his head and restores him back to life - with the drive to mate with as many women as possible. Dennis witnesses this and tells Press and Laura what he saw, joining them in their mission. Patrick begins impregnating as many women as he can, hiding his victims and up to twenty children at the shed.
Laura is ordered to activate Eve's alien DNA so she can telepathically track Patrick, but this makes her volatile and strengthens her alien instincts. Press and Dennis apprehend Patrick at a supermarket, whereupon Patrick becomes aware of Eve. As Patrick is taken to custody, Eve shows signs of being in heat. He demands Laura open Eve's cell and nearly kills her when she refuses, but Press and Dennis drive him off with a special gaseous weapon. Burgess confronts Senator Ross with proof of Patrick's infection and demands help in detaining Patrick. Suspicious that Patrick will instead be killed, Ross deduces that he is at the shed and apologizes for treating his son so coldly. Patrick's human side briefly returns, but while he tearfully embraces his father, the alien DNA violently reasserts itself and kills the Senator. Ross's death completely destroys Patrick's humanity, and he helps his hybrid children to cocoon, so they will soon mature into adults and begin mating themselves to overtake mankind.
Back at the lab, Laura discovers Dennis was not infected because he is a carrier of sickle-cell anemia, as the species lacks immunity to human genetic diseases. While they plan to weaponise this weakness, Eve breaks out of her confinement to find Patrick. Press, Laura and Dennis pursue her, with Burgess and the military following. At the shed, they kill Patrick's offspring while Eve and Patrick transform into their alien forms and begin to mate. The mating stops when Press and Dennis intervene, allowing Eve to break free; Patrick overpowers Eve by performing fellatio, apparently killing her. Press impales him in the back with a pitchfork coated in Dennis' blood, causing Patrick to disintegrate and die.
The military escorts Press, Laura and the injured Dennis away. Eve's lifeless body is loaded into an ambulance, but shortly after, her womb begins to swell rapidly - indicating her survival and impregnation by Patrick - while one of his youngest sons looks on. As the screen cuts to black, Eve's womb bursts and her screaming is heard.
Writer Chris Brancato was working with MGM on The Outer Limits, and knew the studio was interested in making a follow-up to Species. He pitched an idea to executive Greg Foster where this time two hybrid alien women would strike. Foster liked it, but once Brancato went to Species producer Frank Mancuso Jr., he asked to "approach this from a different angle, so that we don't have a tired retread of the original, as sequels often are". So Brancato took inspiration from The Manchurian Candidate, where "somebody on a mission comes back, apparently a hero, but actually with some terrible demon inside", and as "the notion of a grand, unexplored place was the planet Mars", he made the first astronaut on Mars – as according to NASA scientists consulted by Brancato, human exploration of Mars was "a possibility – just a very expensive one" – be infected by alien DNA. Mancuso approved the idea, and thus Brancato explored how this new villain was one "for whom we can briefly feel a strange, Wolf Man-like sympathy – he's not responsible for having been turned into a monster" and had him face an alien woman similar to Sil, raising the doubt on whether they would battle or mate. As Natasha Henstridge was unconfirmed to return, Brancato wrote the new female, Eve, as if it was "either Natasha or a similarly beautiful woman". Henstridge still liked the script enough to sign for the sequel. Brancato decided to bring back two of the surviving characters from Species, Michael Madsen's Press Lennox and Marg Helgenberger's Dr. Laura Baker feeling they "were essential to bring the audience back in", but knowing Forest Whitaker was probably too busy to return as Dan Smithson, he wrote a similar African American character in the one eventually portrayed by Mykelti Williamson. MGM had another script done simultaneously to Brancato's, which reportedly explored the cliffhanger at end of Species where rats were infected after eating Sil's remains. Mancuso brought in to direct Peter Medak, responsible for the 1980 horror film The Changeling.
The nature of the alien species is explored to a slightly greater extent in the second film. A professor claims that they originated in the Large Magellanic Cloud (also called the Magellanic Galaxy), due to it apparently being the only other place carbon-based life forms have been discovered. It is also stipulated that they were a "cancerous" race that visited Mars millions of years ago and annihilated all life on its surface (which is described in the film as being Earth-like at that time) before leaving a remnant of their own DNA in its soil. This DNA was intended to be picked up by other visitors so that their species could continue to infect other inhabited planets. The Species basically appear to be bipedal (humanoid) forms. Unlike other aliens in the Species series, however, Patrick has two types of alien forms, and Patrick's alien form for combat (so-called 'Fighting Patrick') is quadrupedal (as opposed to bipedal, like Patrick's form for copulation and Eve's form), bigger, and more 'brutish' in appearance than Eve. His second stage appearance is also similar to the xenomorphs of the Alien films; both were designed with input from H. R. Giger.
On April 10, 1998 in 2510 theatres, the film finished at $7.2 million, ranking number four on its opening weekend. Domestically, the film grossed only $19.6 million from its $35 million budget and $26,817,565 overseas, making the film a box office flop.
The film received notably worse reviews than its predecessor, currently holding a 9% approval rating at Rotten Tomatoes based on 30 reviews (3 positive, 27 negative). Dwayne E. Leslie from Box Office Magazine gave the film 1 out of 5 stars calling it "a sequel that doesn't measure up", also heavily criticizing the film's predictable and open ending. Joe Leydon from Variety magazine called the film "a half-baked rehash". He praised the special effects and technical aspects of the film but added "that's not nearly enough to camouflage the inherent crumminess." James Berardinelli described the film as awful but added "there's enough blood, gore, simulated sex, and bare flesh to prevent it from ever becoming boring".
In a 2004 interview, co-star Michael Madsen expressed his opinion on this film saying "Species II was a crock of shit. There are a number I'm not very proud of. The movie studios can't mind that much, as they haven't contacted me to tell me off about it. I'm honest – if I've made a bad movie, I want my fans to know what they're letting themselves in for."
In the DVD commentary director Peter Medak highly praised the films' special effects. He expressed his opinion that audiences had too much expectation as this was a very different sequel due to not continuing from the story with the alien-infected rat that survived the finale, which hinted at a sequel in the 1995 original. Medak also admitted being uncomfortable with the amount of nudity in the film but said it was for the purpose of the story.
To coincide with the movie, McFarlane Toys released an Eve and Patrick (in their alien form) action figure as part of their inaugural series of Movie Maniacs action figures. Both action figures came with a replica of the film's poster with skulls and bones base. Eve came with an alternate head. Two Eve action figures were produced which was dubbed the PG and R rated version. The R rated Eve action figure (in her alien form) had nipples on her breasts while the PG figure didn't. The R rated figure was released only in comic book and other collectable stores while the PG figure was released in toy stores. Another thing noticeable about the figures was their facial expressions.
As with the first film, Yvonne Navarro wrote a novelization based on the original screenplay which gives plot and character details not seen in the film. For example, the book tells how, due to limited knowledge of the outside world, Eve does not know if Superman is a real life personality or not. It is also hinted that she was able to learn a degree of martial arts by watching old action movies.
In the film, Eve is shot by soldiers, but after being briefly incapacitated her body regenerates and she continues to escape. Soldiers continue to shoot at her, but Eve manages to run past them; why she is unharmed is left unexplained. The book explains that her skin adapts (in a way similar to how her body adapts to the gas test earlier in the film), becoming bulletproof.
Other details in the book that do not appear in the film include an earlier escape attempt by Eve and Patrick discovering new senses in a restaurant with his fiancé. In the novel, the debutante is a young, sexy, brown-eyed blonde, whereas in the film, she is an older woman who is a brunette. The debutante's sister in the novel isn't her sister but her best friend from college that they often engaged in sexual games that involved seducing men.
Other events that occurred in the novel that occurred in the movie happened before or after other events. For example, Patrick does not encounter the debutante at the fundraiser until after Orinsky is killed by him, and Cromwell is not visited by Laura and Press until they discover Orinsky's corpse.