Theory and Analysis:Eva-03 and Bardiel
Bardiel in the Entry Plug
During the battle against Bardiel in Episode 18, the Angel physically prevents Eva-03's Entry Plug from being ejected, along with its pilot, Toji Suzuhara. In addition, Eva-01, under control of the Dummy System, does not stop destroying the infected Eva-03 until it removes and crushes the entry plug. That the entry plug bleeds red fluid (blood) instead of orange LCL when crushed and the visible presence of the Angel's fungus-like growths inside the Entry Plug show that some of the Angel's biomass was physically present within the Entry Plug.
Contact with Toji
No direct evidence, although Toji being partially covered in the Angel growths and his presence in a train scene along with Shinji and Rei afterwards suggest that Bardiel and Toji had contact.
It's possible that the reason Bardiel traps the entry plug is because it is intelligent enough to realize that the the eva might not be able to move without a plug in place.
Bardiel may have needed to infect the entry plug (and possibly make contact with Toji) as part of the infection process, and the plug appears to contain part of the Angel's biomass when seen in its wrecked state. This makes it probable that the plug had to be crushed to kill the Angel.
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