Alphys

Dr. Alphys (/ˈæl.fiːz/ or /ˈæl.fɪs/; AL-feez, AL-fis) is a female, reptile-like monster living in the lab in western Hotland. She is the incumbent Royal Scientist, a position she earned after the death of her predecessor by creating a robot with a SOUL.

Appearance
Alphys appears to be a reptilian monster of similar height to the protagonist. She has deeply yellow skin, wears glasses, and normally dons 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 and shy recluse that has a fondness for human anime and manga. Alphys lacks self-confidence with what she does. She often stutters, and appears to have developed a deep fascination with the protagonist after having watched them through the cameras spread throughout the Underground. She has romantic feelings for Undyne, which she believes to be 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 whom 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.

Alphys 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 Lab during the Pacifist Route. The effect of this issue has left her with a severe depression; in the story, it is hinted that Alphys may be suicidal.

Neutral Route
Undyne briefly mentions Alphys in the scene immediately before her fight with the protagonist, 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. At 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 whom 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 protagonist 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 protagonist 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. Mettaton states that 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 protagonist spared Mettaton, Alphys is relieved to see that he survived and simply ran out of battery power. If the protagonist killed Mettaton, Alphys gets increasingly nervous, though tries to calm herself, saying that she can always build a new robot.

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.

True Pacifist Route
In a second playthrough, or if the protagonist 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.

True Lab
Returning to the lab at Papyrus's 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's 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, Alphys 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; melting together due to the incompatibility of the concentrations of determination that were injected, reacting erratically due to differences in monster material 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 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. Mettaton then appears and encourages Undyne and Alphys to kiss, saying that "THE AUDIENCE IS DYING FOR SOME ROMANTIC ACTION!!!". 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 and defends them from Flowey's attacks, before Flowey absorbs her SOUL along with almost everybody's, allowing Flowey to become Asriel. The protagonist calls for Alphys's 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's 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 Onionsan. She receives a kiss on the cheek from Undyne and faints from the passion and power (9999 damage).

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

If the Genocide Route is completed, then Alphys's efforts were all for nothing, as the world is destroyed.

If the Genocide Route is aborted by not killing all the monsters in Hotland and the CORE, 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 due to their actions, becoming a hero to the monsters. She laments that she should have killed the protagonist when she had the chance.

Mettaton
Before the events of Undertale, Mettaton (as a ghost) started a Human Fan Club. The only person who joined was Alphys, who showed Mettaton designs of a robot she wanted to build for him. Mettaton ultimately joined Alphys for the body, even leaving Napstablook behind.

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 do not 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, but she is romantically interested in her as well. Alphys respects her for being brave, confident and strong: everything Alphys isn't. She attempts to make herself look cool in front of Undyne, afraid she will think she is a loser. Mettaton has stated she writes Undyne's name in the margins of her notes, names programming files after her and has even written stories about them sharing a domestic life.

Undyne is known to hang out at her lab, where Alphys has shown her anime, claiming to be human history movies (and leading Undyne into thinking anime is real.)

True Pacifist Route
Upon learning her feelings are shared, their relationship grows. After receiving Undyne's letter and going on a date with the protagonist (as Undyne had not signed the letter, so Alphys thought the protagonist had written it), Alphys admits she is in love with Undyne, which leads her to roleplay so she can gain confidence to confess her feelings. Undyne ends up overhearing her, and Alphys admits she lied about herself to make herself look better. Undyne responds by telling her that she does not care about what Alphys is into; she likes her because she is passionate.

She and Undyne later join in breaking up the fight between Asgore and the protagonist. Alphys finally confesses her feelings, which are reciprocated by Undyne. The two try to kiss, but Toriel stops them from doing so in front of the protagonist.

In the True Pacifist Ending Credits, Undyne is shown giving Alphys a kiss on the cheek while on the beach. Alphys blushes profusely and comically falls over.

Papyrus
Alphys's observed interactions with Papyrus are limited, but it is clear they've met on the internet before at the very least, as they are mutual followers of each other on the Underground's social network. It is unknown if she has linked his online persona to his real self, as she does not 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 seems to know Sans, as hinted by the conversation in the True Pacifist Ending Epilogue, where Sans attempts to jinx Alphys but fails. Alphys seems to have knowledge of Sans's pun-making personality, and thus Papyrus questions it, asking " WAIT, ALPHYS, I DIDN'T KNOW YOU KNEW SANS. ", which causes Alphys to get nervous, but Sans quickly answers the question with " doesn't everyone? ".

Sans is also implied to come from a scientific background, so it may be possible the two used to work with each other.

The protagonist
Alphys holds great admiration for the protagonist 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 the protagonist 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 the protagonist's offer of a date much later, thinking the letter Undyne had written to her was from the protagonist. After an encounter with Undyne at the dump, she comes clean that she'd gone out with the protagonist primarily to let them down gently in one fashion or another, as she is not interested in them.

On a Genocide Route that was aborted at Mettaton NEO, however, Alphys holds no positive feelings for the protagonist, 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 protagonist chooses him as the answer to the trivia question 'who does Dr. Alphys have a crush on?'. Mettaton tells the protagonist that Alphys built him in an attempt to impress Asgore, saying 'Why would someone outfit an amusement robot with brutal combat capabilities? Simple. To impress Mr. Asgore Dreemurr of course!'. She calls him "Mr. Dreamy".

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 Asgore and Toriel are cute together.)

Toriel
Alphys does not appear to know of Toriel's existence until after 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.

The Family Ending with Alphys befriended confirms that she finds Toriel attractive. She thinks that she and Asgore are still an excellent match despite their break-up and Toriel's lingering disgust for him, though she will accept the unlikeliness of them getting back together if it is pointed out to her.

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 have not seen much of her since she became Royal Scientist.

Trivia

 * When attempting to name the Fallen Human "Alphys", the response becomes "D-Don't do that" and prevents the name from being used. However, naming the fallen human "Alphy" gives a confused "....OK????" and is allowed.
 * There is one instance where Undyne use the possessive case of Alphy.
 * Alphys is an anagram of "shy pal", likely where her name came from.
 * It is also possible that Alphys' name was derived from the word "alpha", alluding her role as the Royal Scientist.
 * Throughout the game, Alphys says her favorite anime is "Mew Mew: Kissy Cutie" and describes a few details about the series. It is possible that this is a reference to Tokyo Mew Mew (also known as Mew Mew Power in North America) a typical romance magical girl anime. This is further supported by posters in her lab like the one with a female character similar to TMM's protagonist, Ichigo Momomiya (Zoey Hanson in the English dub), and the one with a logo resembling TMM's title.
 * Before entering the True Lab, the "trash can" can be examined, containing a note in a "strange kind of handwriting" that says "I KNOW WHAT YOU DID." It is unknown who the note is from, though it is speculated to be Flowey by some fans, possibly as part of his plan to get all of the protagonist's friends in one place by pushing Alphys to reveal her secrets.
 * Alphys is the only major monster in the game who is not fought by the protagonist, and thus it is impossible for them to kill her. However, it is implied that she is driven to suicide in certain Neutral Endings (such as when Undyne, Mettaton, or both are killed), indirectly caused by the protagonist. Also, Alphys can be safely assumed to be killed, along with the rest of the world, at the end of a Genocide run.
 * In conjunction with the above, Alphys's full combat capabilities are unknown. The only hints come at the end of a True Pacifist route, where she generates a wall of electricity to protect the protagonist's SOUL from Flowey's bullets - in the subsequent battle against Asriel, Alphys's Lost Soul form reuses some of Mettaton EX's attacks.
 * A reoccurring mistake with Alphys is her number of buckteeth switching from two to three.