Alphys

Alphys (pronounced Al-feez) is a monster that appears to be reptilian. She is the Royal Scientist, a position she earned by creating a robot with a soul. She is first met in the Lab within Hotland, and appears to live there as well.

Appearance
Alphys appears to be a stout reptile-monster of similar height to Frisk. She has yellowish-brown skin, and wears a white lab coat. She does, however, have a black and white polka dot dress which she wears for special occasions.

Personality
Alphys is a nerdy, shy, recluse that takes a fondness to anime and comic books. She stutters often, and appears to have developed a large fascination with the main character after having watched them through the cameras spread throughout the Underground. She has romantic feelings for Undyne, which she believed to have been unrequited, although this proves to be untrue in the True Pacifist Route. When the answer of "Asgore" is given in Mettaton's quiz question asking who she has a crush on, she displays a similar reaction as to the answer of "Undyne", showing she bears some attraction towards Asgore as well.

She has a hidden side of herself that is filled with guilt and insecurities about herself and her accomplishments. In particular, she is unintentionally responsible for the miserable existences of Flowey and the Amalgamates. The majority of this side of her is revealed in the True Laboratory.

Neutral Route
Undyne briefly mentions Alphys in the scene immediately before her fight with the player, saying that 'Alphys's history books made [her] think humans were cool' (it is later revealed that the history books are actually manga). If the protagonist befriends Undyne, she will often talk about Alphys in her phone calls. In the Garbage Dump, Undyne reveals that they first met there. When they first met, Undyne noticed Alphys 'staring into the abyss' and appearing 'contemplative', so she asked her about the abyss, surprising Alphys, who went on to talk about where it led to, captivating Undyne and beginning their friendship.

Alphys herself meets the protagonist in her lab. She explains that she has been watching the protagonist through cameras hidden throughout the Underground, explaining the large screen in the lab that is focused on their head. She informs them about Mettaton, who appears to be trying to kill the human protagonist. Mettaton bursts through a wall and forces the protagonist into a quiz show; Alphys gives out the letters of the correct answers to the protagonist, but Mettaton notices when she answers a question about one of her favorite video games herself, and ends the quiz shortly after asking who Alphys has a crush on.

Alphys offers to give her phone number to the protagonist, but she notices that their cell phone is old and quickly upgrades it, giving it texting, a key chain, links to two dimensional boxes and access to the Underground's internet, even signing them up for the monsters' social network. After explaining the upgrades, she rushes into her lab's "bathroom".

During the protagonist's journey through Hotland, Alphys frequently updates her status online, eventually calling them to provide assistance and information regarding the puzzles in the area, but sometimes she calls at the wrong time. She stops posting status updates when she realizes that the protagonist is receiving them on their phone. Mettaton harasses the protagonist in several deathtraps, but each time, Alphys informs the protagonist of a phone upgrade that helps them. If the player fails any of Mettaton's challenges, Alphys blames herself for failing to help, but Mettaton lets the protagonist go, claiming that Alphys saved the protagonist, or otherwise calling a commercial break.

Alphys guides the protagonist through the Core, but she has trouble helping them due to the changing layout of the Core. If the player chooses not to follow her directions, she becomes worried about their trust in her.

When they reach the end of the Core, Mettaton reveals that Alphys inserted herself into the protagonist's journey to make herself feel useful: she activated the Hotland and Core's various puzzles and traps, disabled the Core's elevator, and she got Mettaton to give the protagonist trouble, all so that she could intervene later and give the impression that she was helping. Mettaton, having betrayed Alphys, locks himself in with the protagonist to kill them and take their soul to leave for the surface. Alphys tells the protagonist to flip Mettaton's switch, making him vulnerable as well as willing to give the performance of his life, allowing the protagonist to win the battle.

After the battle, Alphys comes to Mettaton's body. If the player spared Mettaton then Alphys is relieved to see that he survived and simply ran out of battery power.

Alphys catches up with the protagonist before they take the elevator to New Home, and admits to having acted dishonestly to the protagonist. She tells them that to pass through the barrier, they need to take Asgore's soul by killing him. She then leaves.

In many neutral endings, Alphys is said to have disappeared, leaving Undyne or Mettaton distraught, with the implication being that she commited suicide. If the protagonist befriended Papyrus and Undyne, then Alphys is said to be alive and attempting to research alternative methods of leaving the Underground, though Undyne notices her feeling bothered about something.

True Pacifist Route
In a second playthrough, or if the player loads their save file and it meets the requirements for the true pacifist route, Undyne asks the protagonist to deliver a letter to Alphys.

Alphys is reluctant to receive the letter, as she has received many angry letters. She mistakes the protagonist as the writer of the letter and goes on a 'date' with them, going to the garbage dump and bumping into Undyne. She tells her the truth about her 'scientific' activities, which are actually her hobbies. Papyrus takes Alphys out for a lesson in self-confidence, but he ends it early and sends her home.

Neutral ending, with Alphys befriended
With Alphys befriended, if the player ends the game without visiting the True Lab, then Alphys will talk to the protagonist in her phone call, telling them that Mettaton is doing OK and that she is attempting to find an alternative way to leave the Underground, with Toriel actually checking that she's working. No mention is made of her true experiments.

True Lab
Returning to the lab at Papyrus' recommendation, the protagonist finds a note from Alphys which tells them that she will be facing her own mistakes. The note directs the protagonist to the True Lab's entrance to find out the truth, in case she never returns. In the True Lab, the protagonist learns of Alphys' experiments and restores the power. Alphys appears and calms down the amalgamates, who are the living victims of her experiments. She thanks the protagonist for coming to help, telling them that she feared that instead of telling the truth, she would run away or 'do something... Cowardly.' She gives a summary of her experiments, admitting that the protagonist probably already knew what she did.

Studying the nature of souls at Asgore's request, she isolated a power she named "determination" and injected it into dying monsters to try and preserve their souls after death, but the injections saved their lives instead. Before she returned the monsters to their families, their bodies shortly manifested side effects of losing physicality and melted together due to the incompatibility of the concentrations of determination that were injected reacting erratically due to differences in monster bodily composition. Alphys fell into shame upon this discovery, eventually becoming unwilling and fearful to inform the monsters' families of what happened, and kept her failure a secret to everybody.

Having opened the True Lab, Alphys declares that she will reveal the truth about her experiments, and that with her friends' support it will be easier for her to do this. She leaves the lab with the amalgamates and returns them to their families.

True Pacifist Ending
Alphys joins Undyne in breaking up the fight between Asgore, the protagonist and Toriel. Alphys and Undyne comfort Asgore, advising him to pursue a romantic relationship with someone else. The two try to kiss but Toriel stops them from doing so.

It turns out that Papyrus called the protagonist's friends at the suggestion of a talking flower. Just as Alphys realizes that the flower was one of her experiments, Flowey binds her and everyone else with vines. Alphys supports the protagonist before Flowey absorbs her soul along with almost everybody's, allowing Flowey to become Asriel. The protagonist calls for Alphys' soul within Asriel and saves her, and her friendship with the protagonist resonates with Asriel, eventually getting him to stop fighting. Asriel learns the protagonist's name - Frisk - and passes this on to Alphys' soul. Her desire to leave the underground (which she shares with every monster) is used by Asriel to destroy the barrier before he releases them.

Alphys regains consciousness along with Frisk's other friends, remembering little about what had just happened. She upgrades Toriel's phone, allowing her to send text messages, and tells the truth about her to Asgore and Toriel; Asgore feels sad for not knowing and Toriel fires her from the position of Royal Scientist.

She tells Undyne that with their newly gained freedom, she will 'stay inside and watch anime like a total loser!' Asgore asks what anime is, and Alphys gets Frisk to help her describe it to Asgore. She passes her phone to Asgore to show an example of anime, realizing too late that it shows two robots in a romantic relationship.

Leaving the Underground, Alphys joins Undyne, who leaves to check on Papyrus. In the credits, she is seen at the beach, with Undyne, the Lesser and Greater dog, the Nice Cream seller and Onion-san. She receives a kiss on the cheek from Undyne and faints.

Genocide Route
Alphys receives a call from Undyne, urging her to evacuate the monsters. She does so, and it is implied that they were taken to the True Lab where they learned about her true experiments. However, she is unsuccessful in evacuating a few people, including the spider and the MTT-Brand Burger Emporium's employee.

If the player completes the Genocide in full then Alphys' efforts were all for nothing, as the world is destroyed.

If the player aborts their Genocide at Mettaton NEO, then Alphys is selected to lead the surviving monsters. Sans finds the protagonist's phone number and passes his phone to Alphys, who tells the protagonist that although she hates them, she ironically had to become a better person, becoming a hero to the monsters. She tells them that she should have killed the protagonist when she had the chance.

Mettaton
Mettaton is very grateful to Alphys as she created his body, but he does lose patience with her every so often.

Neutral Route
During his 'malfunctioning' act, he helps Alphys not only by tormenting the protagonist, but by improvising if things don't go as intended, and he reminds Alphys of what to say.

Alphys cares greatly for Mettaton, and quickly forgives him for actually trying to kill the protagonist himself, worrying about him after the battle.

Undyne
Alphys is friends with Undyne, though she is romantically interested in her as well and strikes up a relationship with her after the date with Frisk upon learning her feelings are shared.

Papyrus
Alphys's observed interactions with Papyrus are limited, but it's clear they've met on the internet before at the very least, as they're mutual followers of each other on the Underground's social network. It's unknown if she's linked his online persona to his real self, as she doesn't seem to recognize him when he shows up during the date. At the end of the date with Alphys, Papyrus gives Alphys training to be happy with who she is.

Sans
Alphys knows Sans to some extent as she's familiar with him in the true pacifist epilogue, but even the game is unclear on precisely how they met or to what capacity, giving the answer of "doesn't everybody know Sans?"

Frisk
Alphys holds great admiration for the human and their adventure through the Underground, tracking them from the very second they exit the Ruins through a variety of cameras hidden throughout the flora and natural features of the areas through which Frisk travels. This eventually culminates in her attempt to self-insert herself into the human's adventure as a savior, which she later admits to being a very hackneyed attempt at making herself feel better. She accepts Frisk's offer of a date much later, thinking the letter Undyne had written to her was from Frisk, but after an encounter with Undyne at the dump she comes clean that she'd gone out with Frisk primarily to let them down gently in one fashion or another as she's not interested in them (and apparently is the only person she's not interested in to some capacity, as the only answer in Mettaton's quiz that doesn't imply her attraction towards an individual is "The human").

On a No Mercy route that was aborted at Mettaton NEO, however, Alphys holds no positive feelings for Frisk, regarding them as a monster that she should have killed when she had the chance.

Asgore
Alphys has a crush on Asgore, as is revealed if the player chooses him as the answer to the trivia question 'who does Dr. Alphys have a crush on?'. Mettaton tells the player that Alphys built him in an attempt to impress Asgore, saying 'Why would outfit an amusement robot with brutal combat capabilities? Simple. To impress Mr. Asgore Dreemur of course!'. In the True Pacifist ending, where Alphys and Undyne are in a romantic relationship, Alphys indicates that she has moved on from her crush on Asgore due to her feelings for Undyne, though she does remark that he and Toriel are cute together.

Toriel
Alphys does not appear to know Toriel, or even know of Toriel, until meeting her in the True Pacifist ending. She does make friends with Toriel fairly easily, though, despite being fired from the position of Royal Scientist by her after she learns of Alphys's determination experiments and their horrific results. Alphys is very amused by Toriel's questioning of people finding her attractive, a likely reference to the immensely positive fan-reception of Toriel after the demo, and thinks that she and Asgore are still a very good match despite their break-up and Toriel's lingering disgust for him.

Bratty and Catty
Alphys used to live on their street. She was like a big sister to them and took them on trips to the dump to find cool junk. They haven't seen much of her since she became Royal Scientist.

Trivia

 * If you type in her name when you are choosing a name on the Start screen, she will say "D-Don't do that", and bar access from using her name. Removing one letter to place your name as "Alphy", though, gives a confused "....OK????" and is allowed.
 * Before you enter the True Lab, you can view Alphys's trash can, which contains a note in "weird hand writing" that says I KNOW WHAT YOU DID.
 * Alphys is the only major monster in the game who is impossible for the player to kill. The closest they can come is implicitly driving her to suicide in certain Neutral Endings, although she's implied to be killed with the rest of the world at the end of a Genocide Route.
 * In conjunction with the above, Alphys's full combat capabilities are unknown. The only hints come in the end of a True Pacifist route, where she generates a wall of electricity to protect the player's SOUL from Flowey's bullets - in the subsequent battle against Asriel, Alphys's Lost Soul form reuses some of Mettaton EX's attacks.