[Abridged] The Lupus I cloud is found between the Upper-Scorpius and the Upper-Centaurus-Lupus sub-groups, where the expanding USco HI shell appears to interact with a bubble currently driven by the winds of the remaining B-stars of UCL. We investigate if the Lupus I molecular could have formed in a colliding flow, and how the kinematics of the cloud might have been influenced by the larger scale gas dynamics. We performed APEX 13CO and C18O observations of three parts of Lupus. We compare these results to the atomic hydrogen data from the GASS HI survey and our dust emission results presented in the previous paper. Based on the velocity information, we present a geometric model for the interaction zone between the USco shell and the UCL wind bubble. We present evidence that the molecular gas of Lupus I is tightly linked to the atomic material of the USco shell. The CO emission in Lupus I is found mainly at velocities in the same range as the HI velocities. Thus, the molecular cloud is co-moving with the expanding USco atomic Hi shell. The gas in the cloud shows a complex kinematic structure with several line-of-sight components that overlay each other. The non-thermal velocity dispersion is in the transonic regime in all parts of the cloud and could be injected by external compression. Our observations and the derived geometric model agree with a scenario where Lupus I is located in the interaction zone between the USco shell and the UCL wind bubble. The kinematics observations are consistent with a scenario where the Lupus I cloud formed via shell instabilities. The particular location of Lupus I between USco and UCL suggests that counter-pressure from the UCL wind bubble and pre-existing density enhancements, perhaps left over from the gas stream that formed the stellar subgroups, may have played a role in its formation.
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