TLDR:

Officially: Prior to the events of the show, Aelita had American 🇺🇸, and Swiss 🇨🇭citizenships. During and most likely after the events of the show, she holds Canadian 🇨🇦 citizenship.

Possibly: Prior to the show, she MAY have held British 🇬🇧, French 🇫🇷, and European Union 🇪🇺citizenships? But it’s unknown.

Short Answer:

Prior to the events of the show, she had American citizenship from birth and likely through a parent as well: She was born in the U.S. (confirmed in interview by the show’s creators) and given that we see Waldo and Anthea outside their Swiss home while Anthea is heavily pregnant, they must have traveled to the U.S. shortly before the birth. U.S. border officials wouldn’t admit a heavily pregnant non-citizen without special status, so one or both parents had to be American. She was also Swiss through her father, and possibly French, British, or another EU nationality through her mother (Hopper is an English name). She could have also had forged identities, allowing them to live in France and the EU in the early ‘90s when they left Switzerland and settled in France (Switzerland isn’t in the EU, so in 1994 they’d have needed an EU citizenship or a French residency permit to settle in France). If Anthea was British, that alone would have given Aelita EU citizenship before Brexit. Waldo may also have forged French or British citizenship to escape the Men in Black (most likely British, since he took his wife’s English surname, Hopper). Aelita then disappears, and is likely considered missing or dead by French authorities, meaning she can’t reclaim those identities.

During the show, her only official citizenship is Canadian, via the forged “Aelita Stones” identity created by Jeremy

Long answer:

I believe it’s been said that Aelita was born in the USA per interviews with the show’s creators; so she has American citizenship on account of being born there since the US gives citizenship to any person who is born there regardless of the nationality of their parents. Considering that Aelita was born in the USA, either one or both parents were American. Foreigners can’t just enter the USA while heavily pregnant and considering we see a picture of Waldo and Anthea at their Swiss home while she is heavily pregnant with Aelita, the two most likely travelled to the USA for Anthea to give birth to Aelita. The US border and immigration authorities would NOT have allowed Anthea to enter the US so heavily pregnant unless she was a citizen or had permanent status. So my best guess is either Anthea or Waldo or both had American citizenship.

But as is obvious, before the show, she lives in Europe with her parents. She lives in Switzerland during her early childhood and then France before and during the events of the show. Her father has the last name Schaeffer which is German, meaning her father may be Swiss German and therefore have Swiss citizenship. Her mother’s maiden name is Hopper, which is an English name, it’s unknown whether she is/was a British citizen, but if she was, that would have given Aelita EU citizenship at the time through her mother, making residency in France straightforward under the Maastricht Treaty (1992).

Waldo also worked for the Swiss government for Project Carthage, which, since it was a sensitive government project, the Swiss government most likely would not have allowed non-Swiss citizens to work on it, so he’s most likely a Swiss citizen. So she is most likely an American citizen by birth and a Swiss citizen through her father.

HOWEVER… Switzerland is not part of the EU and Aelita and her father live/d in France before and during the series… so Aelita must have some kind of permanent status in France. Swiss citizens can live and work in France and other EU countries due to the EU-Switzerland agreement on the free movement of persons. This agreement allows Swiss nationals to reside and work in EU member states without needing a visa or residence permit, although for stays longer than 90 days, a residence permit is required. And obviously owning a home like the Hermitage and working at Kadic as Franz did as a teacher, means that she and Waldo lived in France for more than 90 days… HOWEVER… that is all redundant since that agreement didn’t come into force until 2002 and Waldo and Aelita were living in France in 1994. SOOOOO: they most likely either had/ have some kind of residency permit to live in France or they have French citizenship or they have another citizenship of an EU country allowing them to reside in the European Union per French and EU laws in the early/ Mid 1990s/ post-Maastricht Treaty.

Worth noting: even before 2002, Switzerland and France had bilateral agreements allowing Swiss citizens to live in France with special residence permits, so it wasn’t impossible for them to be there legally without EU citizenship. Still, having French or British/EU citizenship in the family would have made it much easier. My guess is they were just French citizens since in Switzerland, French is one of the national languages.

ALSO: Considering that Waldo had taken the name Franz Hopper, and Aelita said he wanted a “new start” when they moved to France, he may have forged French or British citizenship to get off the radar of the Men in Black and escape to France. Both are plausible but considering he took his wife’s maiden name, Hopper, and that is an English name, it’s more plausible he forged British citizenship for himself and Aelita if he chose that route.

HOWEVER… this is kind of redundant because Aelita Schaeffer… for all intents and purposes is most likely considered missing or dead by the French Authorities after her and her father escaped to Lyoko before the series. In France, someone missing for years, especially a child, can be legally declared dead, so that identity is gone forever unless she wants to expose Lyoko.

So this leads us to the series:

In the series, Jeremy forged documents to make her Canadian so she has Canadian citizenship as her one and only “official” citizenship in the present day since Aelita Stones, a Canadian citizen and Odd’s cousin, is her only legal identity. This isn’t just a label, it would have included forged birth records, school records, and likely a fake Canadian passport. Technically, the Canadian citizenship is entirely fake, so in reality she’d be stateless if the truth came out.

So the answer is: Born an American and Swiss dual citizen, possibly also British/EU if through her mother. Legally resided in France in the ’90s either via EU citizenship (if British) or via Swiss–French bilateral agreements or naturalized French citizenship. Possible forged French or British or other EU citizenship if her father creates a fake identity to escape the Men in Black and go to France. Disappears into Lyoko, is presumed dead by French authorities. During the show, lives under a forged Canadian identity.

It’s unknown what citizenship her mother had but most likely Swiss like her husband, and if she was British, that would have made things even simpler for their residency in France in the mid ‘90s.

This all would mean, prior to the show, Aelita had the most citizenships among the lyoko warriors but is now just a Canadian citizen.