Clarke went to CoL probably involuntarily and as when she was in Mount Weather will not accepted the brain washing. Knowing clarke, she also must have been trying to destroy the city. The guys in suit who goes after her must have been something like anti-body/anti-virus on ALIE software. But clarke has no defense against them. Came Lexa. How? I was thinking about "love being the strongest weapon" quotes. So my theory is Lexa's attachment to clarke, her love, let the ALIE2.0 into the CoL system somehow. Lexa is ALIE2.0's avatar in CoL. I don't think it was just a figment of clarke's imagination because if they go to that route, then please, rot in hell. I believe we will see clarke and lexa bested ALIE together. I didn't write this to make people keep watching. I, myself will never watch this show live. If anything, i want people to be ready for another goodbye. Because fool me once, shame on you. Fool me twice shame on me.