(Timeline source is suspiciously overly-specific, but it's in the ballpark, so I'll run with it...)
Shinji spends 16 hours in an Angel, contemplating death by asphyxiation, and alternating between panic attacks and hallucinations. Fluke near-death-experience Eva fuckery ensues. The psychological trauma is enough to start tanking his sync rate.
A week and a half later, he's made to crush and mangle his friend by proxy. Understandable rage ensues, and his father orders him rendered unconscious.
Shinji spends the next couple of days in jail. He decides to cut ties and bail on everything. Then another Angel attacks, and he sees innocents get crushed under the decapitated head of Asuka's Eva, followed by Rei's Eva getting wrecked. Kaji guilts him into jumping back into an Eva, where more psychotic-break Eva fuckery gets him absorbed. A month later (subjectively, nothing[?]) it squirts him back out, naked and traumatized. A couple days later, he finds out that Kaji got plugged.
Another week later, Shinji gets to sit impotently and listen to Asuka getting mindfucked. Thereafter, Asuka is clearly very damaged, and falls into a depressive spiral, to which Shinji gets front-row seats.
Half a week later, Rei kills herself to take out an Angel. Misato figures that gross violations of trust are an acceptable method for consoling grief -- Shinji doesn't approve. Then a couple days later, Rei un-dies. Shortly thereafter, Ritsuko reveals that everything they've been doing is a lie, Rei is a creepy quasi-human soul-puppet, and she turns the Ayanami fishbowl into a meaty horror-show in front of him.
Shinji decides that hobo-ing around NERV is preferable to Misato's brand of surrogate parenthood. What few civilian friends decide Tokyo-3 is too dangerous and leave. Shinji is left is an emotional basketcase, bereft of an emotional support network -- simultaneously desperate for and terrified of emotional intimacy.
Then Kowaru shows up one morning, talking like he's auditioning for a role in a Matrix sequel. By evening, he's providing the trappings of close friendship to a boy desperate for them -- mostly by steamrolling Shinji's reticence by acting overly personal/familiar (as a creature with no ego barrier or concept of personal space might do...). The next day, Kowaru unveils his betrayal, surprising absolutely no one (except Shinji). He holds everything hostage, and forces Shinji to kill him (mirroring the proxy maiming of Touji, but for real this time).
Shortly thereafter, Shinji finds out about Asuka's suicide attempt and catatonia.
