Then, the more distant lands were distributed away to individuals, while the 80a territory surrounding the central buildings remained the state's property and was turned into a children's orphanage.

[5][6] In 1944–1945 a partisan headquarter of the Didžioji Kova military district was organized by Jonas Misiūnas-Green Devil in the manor.

In February 1945, Stasys Misiūnas-Old Man led LLA 5th district's headquarters company to permanently settle inside the attics of both laborers houses of the manor.

[5] On March 27 1945, the headquarter was betrayed by the residing orphan Kazys Snieginis and a battle between the NKVD soldiers and partisans commenced.

Surmilavičius was shot on the spot, while Lapinskas was injured, chased, and finally gunned down near the Rusių Ragas [lt] village, choosing to drown himself in the river.

The laborers house of the manor was shelled by the NKVD killing 3 partisans - Juozas Marcinauskas-Pluta, Jonas Markulis-Vaiduoklis and Mykolas Tveraga-Aras during the attack.

S. Misiūnas was injured and managed to initially evade capture, but was caught some days later - both were sentenced to 10 and 5 years in prison respectfully.

NKVD soldiers captured weapons and ammunition, uniforms, typewritter and equipment, radio transmitter and two receivers, over 1,000 chervonets as well as other supplies stored in the headquarter.

[8] Čiobiškis Manor was privately bought by Eugenija Vagnerienė[9] and is being refurbished (2020) to be a hotel, spa and cultural centre.