This study presents an extensive systems-level multi-pathway sustainability assessment of algae biofuel production that demonstrates the necessity of high-value co-products, examines the impact of public policy scenarios, and identifies improvements and pathway directions required for economic viability. Engineering process models for several fuel and co-product pathways were leveraged to perform high fidelity techno-economic analysis. These pathways included: baseline hydrothermal liquefaction; protein extraction followed by hydro thermal liquefaction; fractionation into high-value chemicals with fermentation followed by hydrothermal liquefaction for fuels; and a small-scale first-of-a-kind plant coupled with a wastewater treatment facility. From these models, it was shown that hydrothermal liquefaction as a fuel-only pathway is not economically viable. Likewise, the benefits of coupling with wastewater water treatment are insignificant compared to the impact of reduced facility size resulting in increased capital costs. These models were also used to examine public policy scenarios, uniquely presenting their impact on the breakeven cost of fuel production and sensitivity to scenario assumptions. Specifically, depreciation type was shown to be irrelevant for writeoffs faster than 10 years. Due to discounting, short-term subsidies were found to capture 50% of the subsidy value in 6 years with an additional 24 years required for full subsidy valuation. Integration of a carbon economy was shown to decrease biofuel production costs, particularly for the protein pathway due to the co-product accounting. Finally, a metric of normalized costs was used to compare algal biorefineries to corn and cellulosic ethanol production, showing that algal systems are uniquely different due to significantly higher capital costs, though operational costs are comparable. This work demonstrates that, to reach economic viability, algal biofuel production must either utilize higher value non-fuel co-products or achieve drastic reductions in capital costs.