In 1850, Daukantas retired from his job due to poor health and moved back to Samogitia where he lived in Varniai under the care of bishop Motiejus Valančius for a few years.

He was a prolific writer and worked on a wide range of books – studies on the history of Lithuania, publications of primary historical sources, collections of Lithuanian folklore, Polish–Lithuanian dictionaries, Latin textbook for schoolchildren, primer of the Lithuanian language, Catholic prayer book, agricultural manuals for peasants, translations of classical Roman texts, novel for youth inspired by Robinson Crusoe.

While he was a well read erudite who spent considerable time and effort in obtaining primary sources, his historical works are highly influenced by romantic nationalism and didactically idealize the past.

[7] An analysis of inventories of Skuodas Manor revealed that the family were free peasants – different from serfs in that they had some personal freedoms and paid quit-rent instead of performing corvée.

[21] Daukantas was interested in philology and studied Latin, Russian, and Polish literature, French language, rhetoric, poetry, natural and land law (leges patrias).

[29] He provided a large parchment, signed by Michał Józef Römer as marshal of the szlachta of the Vilna Governorate on 24 August 1820, that described an extensive genealogy of Daukantai family of Olawa coat of arms [pl] that traced back to the late 1500s.

He had to answer questions on a wide variety of subjects, from the law and history of Ancient Rome and impostors of Dmitry of Uglich to theory of taxes and specifics of Russian economy as well as thoughts of Montesquieu and Adam Smith.

[37] Part of the delay was caused by suppression of the Filomat and Filaret secret student societies (Daukantas' name was included on a list of potential members, but there is no evidence that he ever joined them).

[46] Researcher Roma Bončkutė proposed that Daukantas was inspired to write the work after reading The Seasons by Kristijonas Donelaitis, first published by Ludwig Rhesa in 1818.

[56] In March 1837, he transferred to the third department which dealt with all kinds of cases, complaints, and appeals from eastern governorates of the Russian Empire, including Vilna and Kovno.

[62] Afraid of attracting police attention and losing his job, Daukantas kept his historical research a secret and always asked friends and acquaintances not to publish or mention his name.

[64] Even when sending a copy of Būdas senovės lietuvių, kalnėnų ir žemaičių to Teodor Narbutt, Daukantas described the work as if written by an unknown person.

[80] In an 1846 letter to Narbutt, Daukantas complained of poor health which he attributed to long hours spent in cold and damp archives of the Russian Senate.

In September, he obtained an official certificate from a German doctor in Telšiai that at the age of 58 and troubled by many ailments he was unfit to continue his work in Saint Petersburg.

[91] Daukantas moved to Jaunsvirlauka [lv] (German: Neu-Bergfried) in present-day Latvia to live with Petras Smuglevičius, a medical doctor and a relative of painter Franciszek Smuglewicz.

[95] Akelaitis, Valančius, and Daukantas wanted to establish Pakeleivingas, a Lithuanian-language periodical aimed at the ordinary village people, but could not get government's permission.

[105] He wrote his first historical work, Darbai senųjų lietuvių ir žemaičių (Deeds of the Ancient Lithuanians and Samogitians), in 1822 while still a student at Vilnius University.

[111] In 1850, Daukantas reworked it as Pasakojimas apie veikalus lietuvių tautos senovėje (Story of the Deeds of the Ancient Lithuanians) which ended with the death of Grand Duke Vytautas in 1430.

[111] The short chapter on numismatics, which discussed the Lithuanian long currency and earliest coins of the Grand Duchy, retained its scientific relevance until the 1930s.

[124] Daukantas painted an idealized image of ancient Lithuanians who embodied stoic values and lived peacefully in their vast forests until the nobility adopted foreign customs, became lazy, and started exploiting the common folk.

[127] He depicted Grand Duke Vytautas as the great Lithuanian hero while King Jogaila, who initiated the Polish–Lithuanian union in 1385, was a symbol of all ills and evils that later befell Lithuania.

For example, he elaborated on the theory that Lithuanians were descendants of Herules that he took from Albert Wijuk Kojałowicz (though he rejected the legend about Roman Palemonids),[137] praised ancient democracy of Prussian king Widewuto,[138] and used a loose translation of the short story Żiwila by Adam Mickiewicz.

[141] Overall, Daukantas' historical works were mostly influenced by the two-volume Historiae Lituanae by Albert Wijuk Kojałowicz (published in 1650 and 1669) from which he borrowed the structure, content, rhetorical and stylistic elements.

[143] Darbai senųjų lietuvių ir žemaičių had 254 references: 89 to works by August von Kotzebue, 62 to Albert Wijuk Kojałowicz, 29 to Nikolay Karamzin, 15 to Antoni Hlebowicz [pl], and 10 to Teodor Narbutt, in total 31 authors.

Mikalojus Akelaitis, Laurynas Ivinskis, Dionizas Poška, Simonas Stanevičius, Kiprijonas Nezabitauskis, and others are known to have started compiling a dictionary but their works were similarly not published.

[163] In 1841, Tsarist authorities, looking to weaken the Polish culture, allowed Samogitian Diocese to establish parish schools that could teach Lithuanian language.

[164] In 1842, Daukantas published 1,500 copies of Abėcėlė lietuvių, kalnėnų ir žemaičių kalbos (Alphabet of Lithuanian, Highlander, and Samogitian Language).

[166] While the book included the traditional prayers and catechism, it also added short moral teachings (e.g. to respect your parents), seven fables, and 298 Lithuanian proverbs.

[186] In 1847, Daukantas began translating and publishing booklets with agricultural advice in hopes that Lithuanian peasants could improve their economic conditions via more efficient and profitable farming methods.

[191] In the early works, Daukantas wrote in the heavy Samogitian dialect (dounininkai sub-dialect) using plentiful diacritics and archaic words, some even borrowed from Latvian or Prussian.